id	sid	tid	token	lemma	pos
10_1101-436634	1	1	RegTools	regtool	NNS
10_1101-436634	1	2	:	:	:
10_1101-436634	1	3	Integrated	integrate	VBN
10_1101-436634	1	4	analysis	analysis	NN
10_1101-436634	1	5	of	of	IN
10_1101-436634	1	6	genomic	genomic	JJ
10_1101-436634	1	7	and	and	CC
10_1101-436634	1	8	transcriptomic	transcriptomic	JJ
10_1101-436634	1	9	data	datum	NNS
10_1101-436634	1	10	for	for	IN
10_1101-436634	1	11	the	the	DT
10_1101-436634	1	12	discovery	discovery	NN
10_1101-436634	1	13	of	of	IN
10_1101-436634	1	14	splicing	splicing	NN
10_1101-436634	1	15	variants	variant	NNS
10_1101-436634	1	16	in	in	IN
10_1101-436634	1	17	cancer	cancer	NN
10_1101-436634	1	18	1	1	CD
10_1101-436634	1	19	RegTools	regtool	NNS
10_1101-436634	1	20	:	:	:
10_1101-436634	1	21	Integrated	integrate	VBN
10_1101-436634	1	22	analysis	analysis	NN
10_1101-436634	1	23	of	of	IN
10_1101-436634	1	24	genomic	genomic	JJ
10_1101-436634	1	25	and	and	CC
10_1101-436634	1	26	transcriptomic	transcriptomic	JJ
10_1101-436634	1	27	data	datum	NNS
10_1101-436634	1	28	for	for	IN
10_1101-436634	1	29	the	the	DT
10_1101-436634	1	30	discovery	discovery	NN
10_1101-436634	1	31	of	of	IN
10_1101-436634	1	32	splicing	splicing	NN
10_1101-436634	1	33	variants	variant	NNS
10_1101-436634	1	34	in	in	IN
10_1101-436634	1	35	cancer	cancer	NN
10_1101-436634	1	36	Kelsy	Kelsy	NNP
10_1101-436634	1	37	C.	C.	NNP
10_1101-436634	1	38	Cotto1,2,†	Cotto1,2,†	NNP
10_1101-436634	1	39	,	,	,
10_1101-436634	1	40	Yang	Yang	NNP
10_1101-436634	1	41	-	-	HYPH
10_1101-436634	1	42	Yang	Yang	NNP
10_1101-436634	1	43	Feng2,†	Feng2,†	NNP
10_1101-436634	1	44	,	,	,
10_1101-436634	1	45	Avinash	Avinash	NNP
10_1101-436634	1	46	Ramu3	ramu3	NN
10_1101-436634	1	47	,	,	,
10_1101-436634	1	48	Zachary	Zachary	NNP
10_1101-436634	1	49	L.	L.	NNP
10_1101-436634	1	50	Skidmore1,2	skidmore1,2	CD
10_1101-436634	1	51	,	,	,
10_1101-436634	1	52	Jason	Jason	NNP
10_1101-436634	1	53	Kunisaki2	Kunisaki2	NNP
10_1101-436634	1	54	,	,	,
10_1101-436634	1	55	Megan	Megan	NNP
10_1101-436634	1	56	Richters1,2	richters1,2	CD
10_1101-436634	1	57	,	,	,
10_1101-436634	1	58	Sharon	Sharon	NNP
10_1101-436634	1	59	Freshour1,2	Freshour1,2	NNP
10_1101-436634	1	60	,	,	,
10_1101-436634	1	61	Yiing	Yiing	NNP
10_1101-436634	1	62	Lin4	Lin4	NNP
10_1101-436634	1	63	,	,	,
10_1101-436634	1	64	William	William	NNP
10_1101-436634	1	65	C.	C.	NNP
10_1101-436634	1	66	Chapman4	Chapman4	NNP
10_1101-436634	1	67	,	,	,
10_1101-436634	1	68	Ravindra	Ravindra	NNP
10_1101-436634	1	69	Uppaluri5,6	uppaluri5,6	CD
10_1101-436634	1	70	,	,	,
10_1101-436634	1	71	Ramaswamy	Ramaswamy	NNP
10_1101-436634	1	72	Govindan1,7	govindan1,7	CD
10_1101-436634	1	73	,	,	,
10_1101-436634	1	74	Obi	Obi	NNP
10_1101-436634	1	75	L.	L.	NNP
10_1101-436634	1	76	Griffith1,2,3,7	Griffith1,2,3,7	NNP
10_1101-436634	1	77	*	*	NFP
10_1101-436634	1	78	,	,	,
10_1101-436634	1	79	Malachi	Malachi	NNP
10_1101-436634	1	80	Griffith1,2,3,7	Griffith1,2,3,7	NNP
10_1101-436634	1	81	*	*	NFP
10_1101-436634	1	82	†	†	NN
10_1101-436634	1	83	denotes	denote	VBZ
10_1101-436634	1	84	co	co	JJ
10_1101-436634	1	85	-	-	JJ
10_1101-436634	1	86	first	first	JJ
10_1101-436634	1	87	authors	author	NNS
10_1101-436634	1	88	.	.	.
10_1101-436634	2	1	*	*	NFP
10_1101-436634	2	2	denotes	denote	VBZ
10_1101-436634	2	3	corresponding	correspond	VBG
10_1101-436634	2	4	authors	author	NNS
10_1101-436634	2	5	.	.	.
10_1101-436634	3	1	Correspondence	correspondence	NN
10_1101-436634	3	2	to	to	IN
10_1101-436634	3	3	Obi	Obi	NNP
10_1101-436634	3	4	L.	L.	NNP
10_1101-436634	3	5	Griffith	Griffith	NNP
10_1101-436634	3	6	(	(	-LRB-
10_1101-436634	3	7	obigriffith@wustl.edu	obigriffith@wustl.edu	NN
10_1101-436634	3	8	)	)	-RRB-
10_1101-436634	3	9	and	and	CC
10_1101-436634	3	10	Malachi	Malachi	NNP
10_1101-436634	3	11	Griffith	Griffith	NNP
10_1101-436634	3	12	(	(	-LRB-
10_1101-436634	3	13	mgriffit@wustl.edu	mgriffit@wustl.edu	NN
10_1101-436634	3	14	)	)	-RRB-
10_1101-436634	3	15	.	.	.
10_1101-436634	4	1	Affiliations	affiliation	NNS
10_1101-436634	4	2	:	:	:
10_1101-436634	4	3	1	1	CD
10_1101-436634	4	4	.	.	.
10_1101-436634	5	1	Division	Division	NNP
10_1101-436634	5	2	of	of	IN
10_1101-436634	5	3	Oncology	Oncology	NNP
10_1101-436634	5	4	,	,	,
10_1101-436634	5	5	Department	Department	NNP
10_1101-436634	5	6	of	of	IN
10_1101-436634	5	7	Medicine	Medicine	NNP
10_1101-436634	5	8	,	,	,
10_1101-436634	5	9	Washington	Washington	NNP
10_1101-436634	5	10	University	University	NNP
10_1101-436634	5	11	School	School	NNP
10_1101-436634	5	12	of	of	IN
10_1101-436634	5	13	Medicine	Medicine	NNP
10_1101-436634	5	14	,	,	,
10_1101-436634	5	15	St.	St.	NNP
10_1101-436634	5	16	Louis	Louis	NNP
10_1101-436634	5	17	,	,	,
10_1101-436634	5	18	MO	MO	NNP
10_1101-436634	5	19	,	,	,
10_1101-436634	5	20	USA	USA	NNP
10_1101-436634	5	21	2	2	CD
10_1101-436634	5	22	.	.	.
10_1101-436634	6	1	McDonnell	McDonnell	NNP
10_1101-436634	6	2	Genome	Genome	NNP
10_1101-436634	6	3	Institute	Institute	NNP
10_1101-436634	6	4	,	,	,
10_1101-436634	6	5	Washington	Washington	NNP
10_1101-436634	6	6	University	University	NNP
10_1101-436634	6	7	School	School	NNP
10_1101-436634	6	8	of	of	IN
10_1101-436634	6	9	Medicine	Medicine	NNP
10_1101-436634	6	10	,	,	,
10_1101-436634	6	11	St.	St.	NNP
10_1101-436634	6	12	Louis	Louis	NNP
10_1101-436634	6	13	,	,	,
10_1101-436634	6	14	MO	MO	NNP
10_1101-436634	6	15	,	,	,
10_1101-436634	6	16	USA	USA	NNP
10_1101-436634	6	17	3	3	CD
10_1101-436634	6	18	.	.	.
10_1101-436634	7	1	Department	Department	NNP
10_1101-436634	7	2	of	of	IN
10_1101-436634	7	3	Genetics	Genetics	NNP
10_1101-436634	7	4	,	,	,
10_1101-436634	7	5	Washington	Washington	NNP
10_1101-436634	7	6	University	University	NNP
10_1101-436634	7	7	School	School	NNP
10_1101-436634	7	8	of	of	IN
10_1101-436634	7	9	Medicine	Medicine	NNP
10_1101-436634	7	10	,	,	,
10_1101-436634	7	11	St.	St.	NNP
10_1101-436634	7	12	Louis	Louis	NNP
10_1101-436634	7	13	,	,	,
10_1101-436634	7	14	MO	MO	NNP
10_1101-436634	7	15	,	,	,
10_1101-436634	7	16	USA	USA	NNP
10_1101-436634	7	17	4	4	CD
10_1101-436634	7	18	.	.	.
10_1101-436634	8	1	Department	Department	NNP
10_1101-436634	8	2	of	of	IN
10_1101-436634	8	3	Surgery	Surgery	NNP
10_1101-436634	8	4	,	,	,
10_1101-436634	8	5	Washington	Washington	NNP
10_1101-436634	8	6	University	University	NNP
10_1101-436634	8	7	School	School	NNP
10_1101-436634	8	8	of	of	IN
10_1101-436634	8	9	Medicine	Medicine	NNP
10_1101-436634	8	10	,	,	,
10_1101-436634	8	11	St.	St.	NNP
10_1101-436634	8	12	Louis	Louis	NNP
10_1101-436634	8	13	,	,	,
10_1101-436634	8	14	MO	MO	NNP
10_1101-436634	8	15	,	,	,
10_1101-436634	8	16	USA	USA	NNP
10_1101-436634	8	17	5	5	CD
10_1101-436634	8	18	.	.	.
10_1101-436634	9	1	Department	Department	NNP
10_1101-436634	9	2	of	of	IN
10_1101-436634	9	3	Surgery	Surgery	NNP
10_1101-436634	9	4	,	,	,
10_1101-436634	9	5	Brigham	Brigham	NNP
10_1101-436634	9	6	and	and	CC
10_1101-436634	9	7	Women	Women	NNP
10_1101-436634	9	8	’s	’s	POS
10_1101-436634	9	9	Hospital	Hospital	NNP
10_1101-436634	9	10	,	,	,
10_1101-436634	9	11	Boston	Boston	NNP
10_1101-436634	9	12	,	,	,
10_1101-436634	9	13	MA	MA	NNP
10_1101-436634	9	14	,	,	,
10_1101-436634	9	15	USA	USA	NNP
10_1101-436634	9	16	6	6	CD
10_1101-436634	9	17	.	.	.
10_1101-436634	10	1	Department	Department	NNP
10_1101-436634	10	2	of	of	IN
10_1101-436634	10	3	Medical	Medical	NNP
10_1101-436634	10	4	Oncology	Oncology	NNP
10_1101-436634	10	5	,	,	,
10_1101-436634	10	6	Dana	Dana	NNP
10_1101-436634	10	7	-	-	HYPH
10_1101-436634	10	8	Farber	Farber	NNP
10_1101-436634	10	9	Cancer	Cancer	NNP
10_1101-436634	10	10	Institute	Institute	NNP
10_1101-436634	10	11	,	,	,
10_1101-436634	10	12	Boston	Boston	NNP
10_1101-436634	10	13	,	,	,
10_1101-436634	10	14	MA	MA	NNP
10_1101-436634	10	15	,	,	,
10_1101-436634	10	16	USA	USA	NNP
10_1101-436634	10	17	7	7	CD
10_1101-436634	10	18	.	.	.
10_1101-436634	11	1	Siteman	Siteman	NNP
10_1101-436634	11	2	Cancer	Cancer	NNP
10_1101-436634	11	3	Center	Center	NNP
10_1101-436634	11	4	,	,	,
10_1101-436634	11	5	Washington	Washington	NNP
10_1101-436634	11	6	University	University	NNP
10_1101-436634	11	7	School	School	NNP
10_1101-436634	11	8	of	of	IN
10_1101-436634	11	9	Medicine	Medicine	NNP
10_1101-436634	11	10	,	,	,
10_1101-436634	11	11	St.	St.	NNP
10_1101-436634	11	12	Louis	Louis	NNP
10_1101-436634	11	13	,	,	,
10_1101-436634	11	14	MO	MO	NNP
10_1101-436634	11	15	,	,	,
10_1101-436634	11	16	USA	USA	NNP
10_1101-436634	11	17	Abstract	Abstract	NNP
10_1101-436634	11	18	Somatic	Somatic	NNP
10_1101-436634	11	19	mutations	mutation	NNS
10_1101-436634	11	20	in	in	IN
10_1101-436634	11	21	non	non	JJ
10_1101-436634	11	22	-	-	JJ
10_1101-436634	11	23	coding	coding	JJ
10_1101-436634	11	24	regions	region	NNS
10_1101-436634	11	25	and	and	CC
10_1101-436634	11	26	even	even	RB
10_1101-436634	11	27	in	in	IN
10_1101-436634	11	28	exons	exon	NNS
10_1101-436634	11	29	may	may	MD
10_1101-436634	11	30	have	have	VB
10_1101-436634	11	31	unidentified	unidentified	JJ
10_1101-436634	11	32	regulatory	regulatory	JJ
10_1101-436634	11	33	consequences	consequence	NNS
10_1101-436634	11	34	which	which	WDT
10_1101-436634	11	35	are	be	VBP
10_1101-436634	11	36	often	often	RB
10_1101-436634	11	37	overlooked	overlook	VBN
10_1101-436634	11	38	in	in	IN
10_1101-436634	11	39	analysis	analysis	NN
10_1101-436634	11	40	workflows	workflow	NNS
10_1101-436634	11	41	.	.	.
10_1101-436634	12	1	Here	here	RB
10_1101-436634	12	2	we	-PRON-	PRP
10_1101-436634	12	3	present	present	VBP
10_1101-436634	12	4	RegTools	RegTools	NNP
10_1101-436634	12	5	(	(	-LRB-
10_1101-436634	12	6	www.regtools.org	www.regtools.org	NNP
10_1101-436634	12	7	)	)	-RRB-
10_1101-436634	12	8	,	,	,
10_1101-436634	12	9	a	a	DT
10_1101-436634	12	10	free	free	JJ
10_1101-436634	12	11	,	,	,
10_1101-436634	12	12	open	open	JJ
10_1101-436634	12	13	-	-	HYPH
10_1101-436634	12	14	source	source	NN
10_1101-436634	12	15	software	software	NN
10_1101-436634	12	16	package	package	NN
10_1101-436634	12	17	designed	design	VBN
10_1101-436634	12	18	to	to	TO
10_1101-436634	12	19	integrate	integrate	VB
10_1101-436634	12	20	analysis	analysis	NN
10_1101-436634	12	21	of	of	IN
10_1101-436634	12	22	somatic	somatic	JJ
10_1101-436634	12	23	variants	variant	NNS
10_1101-436634	12	24	from	from	IN
10_1101-436634	12	25	genomic	genomic	JJ
10_1101-436634	12	26	data	datum	NNS
10_1101-436634	12	27	with	with	IN
10_1101-436634	12	28	splice	splice	NN
10_1101-436634	12	29	junctions	junction	NNS
10_1101-436634	12	30	from	from	IN
10_1101-436634	12	31	transcriptomic	transcriptomic	JJ
10_1101-436634	12	32	data	datum	NNS
10_1101-436634	12	33	to	to	TO
10_1101-436634	12	34	identify	identify	VB
10_1101-436634	12	35	variants	variant	NNS
10_1101-436634	12	36	that	that	WDT
10_1101-436634	12	37	may	may	MD
10_1101-436634	12	38	cause	cause	VB
10_1101-436634	12	39	aberrant	aberrant	JJ
10_1101-436634	12	40	splicing	splicing	NN
10_1101-436634	12	41	.	.	.
10_1101-436634	13	1	RegTools	RegTools	NNP
10_1101-436634	13	2	was	be	VBD
10_1101-436634	13	3	applied	apply	VBN
10_1101-436634	13	4	to	to	IN
10_1101-436634	13	5	over	over	IN
10_1101-436634	13	6	9,000	9,000	CD
10_1101-436634	13	7	tumor	tumor	NN
10_1101-436634	13	8	samples	sample	NNS
10_1101-436634	13	9	with	with	IN
10_1101-436634	13	10	both	both	DT
10_1101-436634	13	11	tumor	tumor	NN
10_1101-436634	13	12	DNA	DNA	NNP
10_1101-436634	13	13	and	and	CC
10_1101-436634	13	14	RNA	RNA	NNP
10_1101-436634	13	15	sequence	sequence	NN
10_1101-436634	13	16	data	datum	NNS
10_1101-436634	13	17	.	.	.
10_1101-436634	14	1	We	-PRON-	PRP
10_1101-436634	14	2	discovered	discover	VBD
10_1101-436634	14	3	235,778	235,778	CD
10_1101-436634	14	4	events	event	NNS
10_1101-436634	14	5	where	where	WRB
10_1101-436634	14	6	a	a	DT
10_1101-436634	14	7	variant	variant	JJ
10_1101-436634	14	8	significantly	significantly	RB
10_1101-436634	14	9	increased	increase	VBD
10_1101-436634	14	10	the	the	DT
10_1101-436634	14	11	splicing	splicing	NN
10_1101-436634	14	12	of	of	IN
10_1101-436634	14	13	a	a	DT
10_1101-436634	14	14	particular	particular	JJ
10_1101-436634	14	15	junction	junction	NN
10_1101-436634	14	16	,	,	,
10_1101-436634	14	17	across	across	IN
10_1101-436634	14	18	158,200	158,200	CD
10_1101-436634	14	19	unique	unique	JJ
10_1101-436634	14	20	variants	variant	NNS
10_1101-436634	14	21	and	and	CC
10_1101-436634	14	22	131,212	131,212	CD
10_1101-436634	14	23	unique	unique	JJ
10_1101-436634	14	24	junctions	junction	NNS
10_1101-436634	14	25	.	.	.
10_1101-436634	15	1	To	to	TO
10_1101-436634	15	2	characterize	characterize	VB
10_1101-436634	15	3	these	these	DT
10_1101-436634	15	4	somatic	somatic	JJ
10_1101-436634	15	5	variants	variant	NNS
10_1101-436634	15	6	and	and	CC
10_1101-436634	15	7	their	-PRON-	PRP$
10_1101-436634	15	8	associated	associate	VBN
10_1101-436634	15	9	splice	splice	NN
10_1101-436634	15	10	isoforms	isoform	NNS
10_1101-436634	15	11	,	,	,
10_1101-436634	15	12	we	-PRON-	PRP
10_1101-436634	15	13	annotated	annotate	VBD
10_1101-436634	15	14	them	-PRON-	PRP
10_1101-436634	15	15	with	with	IN
10_1101-436634	15	16	the	the	DT
10_1101-436634	15	17	Variant	Variant	NNP
10_1101-436634	15	18	Effect	Effect	NNP
10_1101-436634	15	19	Predictor	Predictor	NNP
10_1101-436634	15	20	(	(	-LRB-
10_1101-436634	15	21	VEP	VEP	NNP
10_1101-436634	15	22	)	)	-RRB-
10_1101-436634	15	23	,	,	,
10_1101-436634	15	24	SpliceAI	SpliceAI	NNP
10_1101-436634	15	25	,	,	,
10_1101-436634	15	26	and	and	CC
10_1101-436634	15	27	Genotype-	Genotype-	NNP
10_1101-436634	15	28	Tissue	Tissue	NNP
10_1101-436634	15	29	Expression	Expression	NNP
10_1101-436634	15	30	(	(	-LRB-
10_1101-436634	15	31	GTEx	GTEx	NNP
10_1101-436634	15	32	)	)	-RRB-
10_1101-436634	15	33	junction	junction	NN
10_1101-436634	15	34	counts	count	NNS
10_1101-436634	15	35	and	and	CC
10_1101-436634	15	36	compared	compare	VBD
10_1101-436634	15	37	our	-PRON-	PRP$
10_1101-436634	15	38	results	result	NNS
10_1101-436634	15	39	to	to	IN
10_1101-436634	15	40	other	other	JJ
10_1101-436634	15	41	tools	tool	NNS
10_1101-436634	15	42	that	that	WDT
10_1101-436634	15	43	integrate	integrate	VBP
10_1101-436634	15	44	genomic	genomic	JJ
10_1101-436634	15	45	and	and	CC
10_1101-436634	15	46	transcriptomic	transcriptomic	JJ
10_1101-436634	15	47	data	datum	NNS
10_1101-436634	15	48	.	.	.
10_1101-436634	16	1	While	while	IN
10_1101-436634	16	2	certain	certain	JJ
10_1101-436634	16	3	events	event	NNS
10_1101-436634	16	4	can	can	MD
10_1101-436634	16	5	be	be	VB
10_1101-436634	16	6	identified	identify	VBN
10_1101-436634	16	7	by	by	IN
10_1101-436634	16	8	the	the	DT
10_1101-436634	16	9	aforementioned	aforementioned	JJ
10_1101-436634	16	10	tools	tool	NNS
10_1101-436634	16	11	,	,	,
10_1101-436634	16	12	the	the	DT
10_1101-436634	16	13	unbiased	unbiased	JJ
10_1101-436634	16	14	nature	nature	NN
10_1101-436634	16	15	of	of	IN
10_1101-436634	16	16	RegTools	RegTools	NNP
10_1101-436634	16	17	has	have	VBZ
10_1101-436634	16	18	allowed	allow	VBN
10_1101-436634	16	19	us	-PRON-	PRP
10_1101-436634	16	20	to	to	TO
10_1101-436634	16	21	identify	identify	VB
10_1101-436634	16	22	novel	novel	JJ
10_1101-436634	16	23	splice	splice	NN
10_1101-436634	16	24	variants	variant	NNS
10_1101-436634	16	25	and	and	CC
10_1101-436634	16	26	previously	previously	RB
10_1101-436634	16	27	unreported	unreported	JJ
10_1101-436634	16	28	patterns	pattern	NNS
10_1101-436634	16	29	of	of	IN
10_1101-436634	16	30	splicing	splicing	NN
10_1101-436634	16	31	disruption	disruption	NN
10_1101-436634	16	32	in	in	IN
10_1101-436634	16	33	known	know	VBN
10_1101-436634	16	34	cancer	cancer	NN
10_1101-436634	16	35	drivers	driver	NNS
10_1101-436634	16	36	,	,	,
10_1101-436634	16	37	such	such	JJ
10_1101-436634	16	38	as	as	IN
10_1101-436634	16	39	TP53	TP53	NNP
10_1101-436634	16	40	,	,	,
10_1101-436634	16	41	CDKN2A	CDKN2A	NNP
10_1101-436634	16	42	,	,	,
10_1101-436634	16	43	and	and	CC
10_1101-436634	16	44	B2	B2	NNP
10_1101-436634	16	45	M	M	NNP
10_1101-436634	16	46	,	,	,
10_1101-436634	16	47	as	as	RB
10_1101-436634	16	48	well	well	RB
10_1101-436634	16	49	as	as	IN
10_1101-436634	16	50	in	in	IN
10_1101-436634	16	51	genes	gene	NNS
10_1101-436634	16	52	not	not	RB
10_1101-436634	16	53	previously	previously	RB
10_1101-436634	16	54	considered	consider	VBN
10_1101-436634	16	55	cancer	cancer	NN
10_1101-436634	16	56	-	-	HYPH
10_1101-436634	16	57	relevant	relevant	JJ
10_1101-436634	16	58	,	,	,
10_1101-436634	16	59	such	such	JJ
10_1101-436634	16	60	as	as	IN
10_1101-436634	16	61	RNF145	RNF145	NNP
10_1101-436634	16	62	.	.	.
10_1101-436634	17	1	Introduction	introduction	NN
10_1101-436634	17	2	.CC	.CC	NFP
10_1101-436634	17	3	-	-	:
10_1101-436634	17	4	BY	by	IN
10_1101-436634	17	5	-	-	HYPH
10_1101-436634	17	6	NC	NC	NNP
10_1101-436634	17	7	-	-	HYPH
10_1101-436634	17	8	ND	ND	NNP
10_1101-436634	17	9	4.0	4.0	CD
10_1101-436634	17	10	International	international	JJ
10_1101-436634	17	11	licensea	licensea	NNS
10_1101-436634	17	12	certified	certify	VBN
10_1101-436634	17	13	by	by	IN
10_1101-436634	17	14	peer	peer	NN
10_1101-436634	17	15	review	review	NN
10_1101-436634	17	16	)	)	-RRB-
10_1101-436634	17	17	is	be	VBZ
10_1101-436634	17	18	the	the	DT
10_1101-436634	17	19	author	author	NN
10_1101-436634	17	20	/	/	SYM
10_1101-436634	17	21	funder	funder	NN
10_1101-436634	17	22	,	,	,
10_1101-436634	17	23	who	who	WP
10_1101-436634	17	24	has	have	VBZ
10_1101-436634	17	25	granted	grant	VBN
10_1101-436634	17	26	bioRxiv	biorxiv	IN
10_1101-436634	17	27	a	a	DT
10_1101-436634	17	28	license	license	NN
10_1101-436634	17	29	to	to	TO
10_1101-436634	17	30	display	display	VB
10_1101-436634	17	31	the	the	DT
10_1101-436634	17	32	preprint	preprint	NN
10_1101-436634	17	33	in	in	IN
10_1101-436634	17	34	perpetuity	perpetuity	NN
10_1101-436634	17	35	.	.	.
10_1101-436634	18	1	It	-PRON-	PRP
10_1101-436634	18	2	is	be	VBZ
10_1101-436634	18	3	made	make	VBN
10_1101-436634	18	4	available	available	JJ
10_1101-436634	18	5	under	under	IN
10_1101-436634	18	6	The	the	DT
10_1101-436634	18	7	copyright	copyright	NN
10_1101-436634	18	8	holder	holder	NN
10_1101-436634	18	9	for	for	IN
10_1101-436634	18	10	this	this	DT
10_1101-436634	18	11	preprint	preprint	NN
10_1101-436634	18	12	(	(	-LRB-
10_1101-436634	18	13	which	which	WDT
10_1101-436634	18	14	was	be	VBD
10_1101-436634	18	15	notthis	notthis	DT
10_1101-436634	18	16	version	version	NN
10_1101-436634	18	17	posted	post	VBN
10_1101-436634	18	18	January	January	NNP
10_1101-436634	18	19	5	5	CD
10_1101-436634	18	20	,	,	,
10_1101-436634	18	21	2021	2021	CD
10_1101-436634	18	22	.	.	.
10_1101-436634	18	23	;	;	:
10_1101-436634	18	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	18	25	:	:	:
10_1101-436634	18	26	bioRxiv	biorxiv	VB
10_1101-436634	18	27	preprint	preprint	NN
10_1101-436634	18	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	18	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	RB
10_1101-436634	18	30	2	2	CD
10_1101-436634	18	31	Alternative	alternative	JJ
10_1101-436634	18	32	splicing	splicing	NN
10_1101-436634	18	33	of	of	IN
10_1101-436634	18	34	messenger	messenger	NN
10_1101-436634	18	35	RNA	RNA	NNP
10_1101-436634	18	36	allows	allow	VBZ
10_1101-436634	18	37	a	a	DT
10_1101-436634	18	38	single	single	JJ
10_1101-436634	18	39	gene	gene	NN
10_1101-436634	18	40	to	to	TO
10_1101-436634	18	41	encode	encode	VB
10_1101-436634	18	42	multiple	multiple	JJ
10_1101-436634	18	43	gene	gene	NN
10_1101-436634	18	44	products	product	NNS
10_1101-436634	18	45	,	,	,
10_1101-436634	18	46	increasing	increase	VBG
10_1101-436634	18	47	a	a	DT
10_1101-436634	18	48	cell	cell	NN
10_1101-436634	18	49	’s	’s	POS
10_1101-436634	18	50	functional	functional	JJ
10_1101-436634	18	51	diversity	diversity	NN
10_1101-436634	18	52	and	and	CC
10_1101-436634	18	53	regulatory	regulatory	JJ
10_1101-436634	18	54	precision	precision	NN
10_1101-436634	18	55	.	.	.
10_1101-436634	19	1	However	however	RB
10_1101-436634	19	2	,	,	,
10_1101-436634	19	3	splicing	splicing	NN
10_1101-436634	19	4	malfunction	malfunction	NN
10_1101-436634	19	5	can	can	MD
10_1101-436634	19	6	lead	lead	VB
10_1101-436634	19	7	to	to	IN
10_1101-436634	19	8	imbalances	imbalance	NNS
10_1101-436634	19	9	in	in	IN
10_1101-436634	19	10	transcriptional	transcriptional	JJ
10_1101-436634	19	11	output	output	NN
10_1101-436634	19	12	or	or	CC
10_1101-436634	19	13	even	even	RB
10_1101-436634	19	14	the	the	DT
10_1101-436634	19	15	presence	presence	NN
10_1101-436634	19	16	of	of	IN
10_1101-436634	19	17	novel	novel	JJ
10_1101-436634	19	18	oncogenic	oncogenic	JJ
10_1101-436634	19	19	transcripts1	transcripts1	NN
10_1101-436634	19	20	.	.	.
10_1101-436634	20	1	The	the	DT
10_1101-436634	20	2	interpretation	interpretation	NN
10_1101-436634	20	3	of	of	IN
10_1101-436634	20	4	variants	variant	NNS
10_1101-436634	20	5	in	in	IN
10_1101-436634	20	6	cancer	cancer	NN
10_1101-436634	20	7	is	be	VBZ
10_1101-436634	20	8	frequently	frequently	RB
10_1101-436634	20	9	focused	focus	VBN
10_1101-436634	20	10	on	on	IN
10_1101-436634	20	11	direct	direct	JJ
10_1101-436634	20	12	protein-	protein-	JJ
10_1101-436634	20	13	coding	code	VBG
10_1101-436634	20	14	alterations2	alterations2	NNP
10_1101-436634	20	15	.	.	.
10_1101-436634	21	1	However	however	RB
10_1101-436634	21	2	,	,	,
10_1101-436634	21	3	most	most	JJS
10_1101-436634	21	4	somatic	somatic	JJ
10_1101-436634	21	5	mutations	mutation	NNS
10_1101-436634	21	6	arise	arise	VBP
10_1101-436634	21	7	in	in	IN
10_1101-436634	21	8	intronic	intronic	JJ
10_1101-436634	21	9	and	and	CC
10_1101-436634	21	10	intergenic	intergenic	JJ
10_1101-436634	21	11	regions	region	NNS
10_1101-436634	21	12	,	,	,
10_1101-436634	21	13	and	and	CC
10_1101-436634	21	14	exonic	exonic	JJ
10_1101-436634	21	15	mutations	mutation	NNS
10_1101-436634	21	16	may	may	MD
10_1101-436634	21	17	also	also	RB
10_1101-436634	21	18	have	have	VB
10_1101-436634	21	19	unidentified	unidentified	JJ
10_1101-436634	21	20	regulatory	regulatory	JJ
10_1101-436634	21	21	consequences3,4,5,6	consequences3,4,5,6	NN
10_1101-436634	21	22	.	.	.
10_1101-436634	22	1	For	for	IN
10_1101-436634	22	2	example	example	NN
10_1101-436634	22	3	,	,	,
10_1101-436634	22	4	mutations	mutation	NNS
10_1101-436634	22	5	can	can	MD
10_1101-436634	22	6	affect	affect	VB
10_1101-436634	22	7	splicing	splicing	NN
10_1101-436634	22	8	either	either	CC
10_1101-436634	22	9	in	in	IN
10_1101-436634	22	10	trans	tran	NNS
10_1101-436634	22	11	,	,	,
10_1101-436634	22	12	by	by	IN
10_1101-436634	22	13	acting	act	VBG
10_1101-436634	22	14	on	on	IN
10_1101-436634	22	15	splicing	splicing	NN
10_1101-436634	22	16	effectors	effector	NNS
10_1101-436634	22	17	,	,	,
10_1101-436634	22	18	or	or	CC
10_1101-436634	22	19	in	in	IN
10_1101-436634	22	20	cis	cis	NN
10_1101-436634	22	21	,	,	,
10_1101-436634	22	22	by	by	IN
10_1101-436634	22	23	altering	alter	VBG
10_1101-436634	22	24	the	the	DT
10_1101-436634	22	25	splicing	splicing	NN
10_1101-436634	22	26	signals	signal	NNS
10_1101-436634	22	27	located	locate	VBN
10_1101-436634	22	28	on	on	IN
10_1101-436634	22	29	the	the	DT
10_1101-436634	22	30	transcripts	transcript	NNS
10_1101-436634	22	31	themselves7	themselves7	NN
10_1101-436634	22	32	.	.	.
10_1101-436634	23	1	Increasingly	increasingly	RB
10_1101-436634	23	2	,	,	,
10_1101-436634	23	3	we	-PRON-	PRP
10_1101-436634	23	4	are	be	VBP
10_1101-436634	23	5	identifying	identify	VBG
10_1101-436634	23	6	the	the	DT
10_1101-436634	23	7	importance	importance	NN
10_1101-436634	23	8	of	of	IN
10_1101-436634	23	9	splice	splice	NN
10_1101-436634	23	10	variants	variant	NNS
10_1101-436634	23	11	in	in	IN
10_1101-436634	23	12	disease	disease	NN
10_1101-436634	23	13	processes	process	NNS
10_1101-436634	23	14	,	,	,
10_1101-436634	23	15	including	include	VBG
10_1101-436634	23	16	in	in	IN
10_1101-436634	23	17	cancer8,9	cancer8,9	NN
10_1101-436634	23	18	.	.	.
10_1101-436634	24	1	However	however	RB
10_1101-436634	24	2	,	,	,
10_1101-436634	24	3	our	-PRON-	PRP$
10_1101-436634	24	4	understanding	understanding	NN
10_1101-436634	24	5	of	of	IN
10_1101-436634	24	6	the	the	DT
10_1101-436634	24	7	landscape	landscape	NN
10_1101-436634	24	8	of	of	IN
10_1101-436634	24	9	these	these	DT
10_1101-436634	24	10	variants	variant	NNS
10_1101-436634	24	11	is	be	VBZ
10_1101-436634	24	12	currently	currently	RB
10_1101-436634	24	13	limited	limit	VBN
10_1101-436634	24	14	,	,	,
10_1101-436634	24	15	and	and	CC
10_1101-436634	24	16	few	few	JJ
10_1101-436634	24	17	tools	tool	NNS
10_1101-436634	24	18	exist	exist	VBP
10_1101-436634	24	19	for	for	IN
10_1101-436634	24	20	their	-PRON-	PRP$
10_1101-436634	24	21	discovery	discovery	NN
10_1101-436634	24	22	.	.	.
10_1101-436634	25	1	One	one	CD
10_1101-436634	25	2	approach	approach	NN
10_1101-436634	25	3	to	to	IN
10_1101-436634	25	4	elucidating	elucidate	VBG
10_1101-436634	25	5	the	the	DT
10_1101-436634	25	6	role	role	NN
10_1101-436634	25	7	of	of	IN
10_1101-436634	25	8	splice	splice	NN
10_1101-436634	25	9	variants	variant	NNS
10_1101-436634	25	10	has	have	VBZ
10_1101-436634	25	11	been	be	VBN
10_1101-436634	25	12	to	to	TO
10_1101-436634	25	13	predict	predict	VB
10_1101-436634	25	14	the	the	DT
10_1101-436634	25	15	strength	strength	NN
10_1101-436634	25	16	of	of	IN
10_1101-436634	25	17	putative	putative	JJ
10_1101-436634	25	18	splice	splice	NN
10_1101-436634	25	19	sites	site	NNS
10_1101-436634	25	20	in	in	IN
10_1101-436634	25	21	pre	pre	NN
10_1101-436634	25	22	-	-	NN
10_1101-436634	25	23	mRNA	mRNA	NNP
10_1101-436634	25	24	from	from	IN
10_1101-436634	25	25	genomic	genomic	JJ
10_1101-436634	25	26	sequences	sequence	NNS
10_1101-436634	25	27	,	,	,
10_1101-436634	25	28	such	such	JJ
10_1101-436634	25	29	as	as	IN
10_1101-436634	25	30	the	the	DT
10_1101-436634	25	31	method	method	NN
10_1101-436634	25	32	used	use	VBN
10_1101-436634	25	33	by	by	IN
10_1101-436634	25	34	the	the	DT
10_1101-436634	25	35	SpliceAI	SpliceAI	NNP
10_1101-436634	25	36	tool10–13	tool10–13	NN
10_1101-436634	25	37	.	.	.
10_1101-436634	26	1	With	with	IN
10_1101-436634	26	2	the	the	DT
10_1101-436634	26	3	advent	advent	NN
10_1101-436634	26	4	of	of	IN
10_1101-436634	26	5	efficient	efficient	JJ
10_1101-436634	26	6	and	and	CC
10_1101-436634	26	7	affordable	affordable	JJ
10_1101-436634	26	8	RNA	RNA	NNP
10_1101-436634	26	9	-	-	HYPH
10_1101-436634	26	10	seq	seq	NN
10_1101-436634	26	11	,	,	,
10_1101-436634	26	12	we	-PRON-	PRP
10_1101-436634	26	13	are	be	VBP
10_1101-436634	26	14	also	also	RB
10_1101-436634	26	15	seeing	see	VBG
10_1101-436634	26	16	the	the	DT
10_1101-436634	26	17	complementary	complementary	JJ
10_1101-436634	26	18	approach	approach	NN
10_1101-436634	26	19	of	of	IN
10_1101-436634	26	20	evaluating	evaluate	VBG
10_1101-436634	26	21	alternative	alternative	JJ
10_1101-436634	26	22	splicing	splicing	NN
10_1101-436634	26	23	events	event	NNS
10_1101-436634	26	24	(	(	-LRB-
10_1101-436634	26	25	ASEs	ASEs	NNP
10_1101-436634	26	26	)	)	-RRB-
10_1101-436634	26	27	directly	directly	RB
10_1101-436634	26	28	from	from	IN
10_1101-436634	26	29	RNA	RNA	NNP
10_1101-436634	26	30	sequencing	sequencing	NN
10_1101-436634	26	31	data	datum	NNS
10_1101-436634	26	32	.	.	.
10_1101-436634	27	1	Various	various	JJ
10_1101-436634	27	2	tools	tool	NNS
10_1101-436634	27	3	exist	exist	VBP
10_1101-436634	27	4	which	which	WDT
10_1101-436634	27	5	allow	allow	VBP
10_1101-436634	27	6	the	the	DT
10_1101-436634	27	7	identification	identification	NN
10_1101-436634	27	8	of	of	IN
10_1101-436634	27	9	significant	significant	JJ
10_1101-436634	27	10	ASEs	as	NNS
10_1101-436634	27	11	from	from	IN
10_1101-436634	27	12	transcript	transcript	JJ
10_1101-436634	27	13	-	-	HYPH
10_1101-436634	27	14	level	level	NN
10_1101-436634	27	15	data	datum	NNS
10_1101-436634	27	16	within	within	IN
10_1101-436634	27	17	sample	sample	NN
10_1101-436634	27	18	cohorts	cohort	NNS
10_1101-436634	27	19	,	,	,
10_1101-436634	27	20	including	include	VBG
10_1101-436634	27	21	SUPPA2	suppa2	ADD
10_1101-436634	27	22	and	and	CC
10_1101-436634	27	23	SPLADDER14,15	SPLADDER14,15	NNP
10_1101-436634	27	24	.	.	.
10_1101-436634	28	1	Many	many	JJ
10_1101-436634	28	2	of	of	IN
10_1101-436634	28	3	these	these	DT
10_1101-436634	28	4	tools	tool	NNS
10_1101-436634	28	5	have	have	VBP
10_1101-436634	28	6	also	also	RB
10_1101-436634	28	7	evaluated	evaluate	VBN
10_1101-436634	28	8	the	the	DT
10_1101-436634	28	9	role	role	NN
10_1101-436634	28	10	of	of	IN
10_1101-436634	28	11	trans	trans	JJ
10_1101-436634	28	12	-	-	JJ
10_1101-436634	28	13	acting	act	VBG
10_1101-436634	28	14	splice	splice	NN
10_1101-436634	28	15	mutations16	mutations16	NN
10_1101-436634	28	16	.	.	.
10_1101-436634	29	1	However	however	RB
10_1101-436634	29	2	,	,	,
10_1101-436634	29	3	few	few	JJ
10_1101-436634	29	4	tools	tool	NNS
10_1101-436634	29	5	are	be	VBP
10_1101-436634	29	6	directed	direct	VBN
10_1101-436634	29	7	at	at	IN
10_1101-436634	29	8	linking	link	VBG
10_1101-436634	29	9	specific	specific	JJ
10_1101-436634	29	10	aberrant	aberrant	NN
10_1101-436634	29	11	RNA	RNA	NNP
10_1101-436634	29	12	splicing	splice	VBG
10_1101-436634	29	13	events	event	NNS
10_1101-436634	29	14	to	to	IN
10_1101-436634	29	15	specific	specific	JJ
10_1101-436634	29	16	genomic	genomic	JJ
10_1101-436634	29	17	variants	variant	NNS
10_1101-436634	29	18	in	in	IN
10_1101-436634	29	19	cis	cis	NNP
10_1101-436634	29	20	to	to	TO
10_1101-436634	29	21	investigate	investigate	VB
10_1101-436634	29	22	the	the	DT
10_1101-436634	29	23	splice	splice	NN
10_1101-436634	29	24	regulatory	regulatory	JJ
10_1101-436634	29	25	impact	impact	NN
10_1101-436634	29	26	of	of	IN
10_1101-436634	29	27	these	these	DT
10_1101-436634	29	28	variants	variant	NNS
10_1101-436634	29	29	.	.	.
10_1101-436634	30	1	Those	those	DT
10_1101-436634	30	2	few	few	JJ
10_1101-436634	30	3	relevant	relevant	JJ
10_1101-436634	30	4	tools	tool	NNS
10_1101-436634	30	5	that	that	WDT
10_1101-436634	30	6	do	do	VBP
10_1101-436634	30	7	exist	exist	VB
10_1101-436634	30	8	have	have	VB
10_1101-436634	30	9	significant	significant	JJ
10_1101-436634	30	10	limitations	limitation	NNS
10_1101-436634	30	11	that	that	WDT
10_1101-436634	30	12	preclude	preclude	VBP
10_1101-436634	30	13	them	-PRON-	PRP
10_1101-436634	30	14	from	from	IN
10_1101-436634	30	15	broad	broad	JJ
10_1101-436634	30	16	applications	application	NNS
10_1101-436634	30	17	.	.	.
10_1101-436634	31	1	The	the	DT
10_1101-436634	31	2	sQTL	sqtl	NN
10_1101-436634	31	3	-	-	HYPH
10_1101-436634	31	4	based	base	VBN
10_1101-436634	31	5	approach	approach	NN
10_1101-436634	31	6	taken	take	VBN
10_1101-436634	31	7	by	by	IN
10_1101-436634	31	8	LeafCutter	LeafCutter	NNP
10_1101-436634	31	9	and	and	CC
10_1101-436634	31	10	other	other	JJ
10_1101-436634	31	11	tools	tool	NNS
10_1101-436634	31	12	is	be	VBZ
10_1101-436634	31	13	designed	design	VBN
10_1101-436634	31	14	for	for	IN
10_1101-436634	31	15	relatively	relatively	RB
10_1101-436634	31	16	frequent	frequent	JJ
10_1101-436634	31	17	single	single	JJ
10_1101-436634	31	18	-	-	HYPH
10_1101-436634	31	19	nucleotide	nucleotide	JJ
10_1101-436634	31	20	polymorphisms	polymorphism	NNS
10_1101-436634	31	21	.	.	.
10_1101-436634	32	1	It	-PRON-	PRP
10_1101-436634	32	2	is	be	VBZ
10_1101-436634	32	3	thus	thus	RB
10_1101-436634	32	4	ill	ill	RB
10_1101-436634	32	5	-	-	HYPH
10_1101-436634	32	6	suited	suit	VBN
10_1101-436634	32	7	to	to	IN
10_1101-436634	32	8	studying	study	VBG
10_1101-436634	32	9	somatic	somatic	JJ
10_1101-436634	32	10	variants	variant	NNS
10_1101-436634	32	11	,	,	,
10_1101-436634	32	12	or	or	CC
10_1101-436634	32	13	any	any	DT
10_1101-436634	32	14	case	case	NN
10_1101-436634	32	15	in	in	IN
10_1101-436634	32	16	which	which	WDT
10_1101-436634	32	17	the	the	DT
10_1101-436634	32	18	frequency	frequency	NN
10_1101-436634	32	19	of	of	IN
10_1101-436634	32	20	a	a	DT
10_1101-436634	32	21	particular	particular	JJ
10_1101-436634	32	22	variant	variant	NN
10_1101-436634	32	23	is	be	VBZ
10_1101-436634	32	24	very	very	RB
10_1101-436634	32	25	low	low	JJ
10_1101-436634	32	26	(	(	-LRB-
10_1101-436634	32	27	often	often	RB
10_1101-436634	32	28	unique	unique	JJ
10_1101-436634	32	29	)	)	-RRB-
10_1101-436634	32	30	in	in	IN
10_1101-436634	32	31	a	a	DT
10_1101-436634	32	32	given	give	VBN
10_1101-436634	32	33	sample	sample	NN
10_1101-436634	32	34	population17–19	population17–19	NN
10_1101-436634	32	35	.	.	.
10_1101-436634	33	1	Recent	recent	JJ
10_1101-436634	33	2	tools	tool	NNS
10_1101-436634	33	3	that	that	WDT
10_1101-436634	33	4	have	have	VBP
10_1101-436634	33	5	been	be	VBN
10_1101-436634	33	6	created	create	VBN
10_1101-436634	33	7	for	for	IN
10_1101-436634	33	8	large	large	JJ
10_1101-436634	33	9	-	-	HYPH
10_1101-436634	33	10	scale	scale	NN
10_1101-436634	33	11	analysis	analysis	NN
10_1101-436634	33	12	of	of	IN
10_1101-436634	33	13	cancer	cancer	NN
10_1101-436634	33	14	-	-	HYPH
10_1101-436634	33	15	specific	specific	JJ
10_1101-436634	33	16	data	datum	NNS
10_1101-436634	33	17	,	,	,
10_1101-436634	33	18	such	such	JJ
10_1101-436634	33	19	as	as	IN
10_1101-436634	33	20	MiSplice	MiSplice	NNP
10_1101-436634	33	21	and	and	CC
10_1101-436634	33	22	Veridical	Veridical	NNP
10_1101-436634	33	23	,	,	,
10_1101-436634	33	24	ignore	ignore	VB
10_1101-436634	33	25	certain	certain	JJ
10_1101-436634	33	26	types	type	NNS
10_1101-436634	33	27	of	of	IN
10_1101-436634	33	28	ASEs	as	NNS
10_1101-436634	33	29	,	,	,
10_1101-436634	33	30	are	be	VBP
10_1101-436634	33	31	tailored	tailor	VBN
10_1101-436634	33	32	to	to	IN
10_1101-436634	33	33	specific	specific	JJ
10_1101-436634	33	34	analysis	analysis	NN
10_1101-436634	33	35	strategies	strategy	NNS
10_1101-436634	33	36	and	and	CC
10_1101-436634	33	37	sets	set	NNS
10_1101-436634	33	38	of	of	IN
10_1101-436634	33	39	hypotheses	hypothesis	NNS
10_1101-436634	33	40	,	,	,
10_1101-436634	33	41	or	or	CC
10_1101-436634	33	42	are	be	VBP
10_1101-436634	33	43	otherwise	otherwise	RB
10_1101-436634	33	44	inaccessible	inaccessible	JJ
10_1101-436634	33	45	to	to	IN
10_1101-436634	33	46	the	the	DT
10_1101-436634	33	47	end	end	NN
10_1101-436634	33	48	-	-	HYPH
10_1101-436634	33	49	user	user	NN
10_1101-436634	33	50	due	due	JJ
10_1101-436634	33	51	to	to	IN
10_1101-436634	33	52	issues	issue	NNS
10_1101-436634	33	53	such	such	JJ
10_1101-436634	33	54	as	as	IN
10_1101-436634	33	55	lack	lack	NN
10_1101-436634	33	56	of	of	IN
10_1101-436634	33	57	documentation	documentation	NN
10_1101-436634	33	58	,	,	,
10_1101-436634	33	59	difficulty	difficulty	NN
10_1101-436634	33	60	with	with	IN
10_1101-436634	33	61	installation	installation	NN
10_1101-436634	33	62	and	and	CC
10_1101-436634	33	63	integration	integration	NN
10_1101-436634	33	64	with	with	IN
10_1101-436634	33	65	existing	exist	VBG
10_1101-436634	33	66	pipelines	pipeline	NNS
10_1101-436634	33	67	,	,	,
10_1101-436634	33	68	limited	limited	JJ
10_1101-436634	33	69	computing	computing	NN
10_1101-436634	33	70	efficiency	efficiency	NN
10_1101-436634	33	71	,	,	,
10_1101-436634	33	72	or	or	CC
10_1101-436634	33	73	licensing	license	VBG
10_1101-436634	33	74	issues20–22	issues20–22	NNP
10_1101-436634	33	75	.	.	.
10_1101-436634	34	1	To	to	TO
10_1101-436634	34	2	address	address	VB
10_1101-436634	34	3	these	these	DT
10_1101-436634	34	4	needs	need	NNS
10_1101-436634	34	5	,	,	,
10_1101-436634	34	6	we	-PRON-	PRP
10_1101-436634	34	7	have	have	VBP
10_1101-436634	34	8	developed	develop	VBN
10_1101-436634	34	9	RegTools	RegTools	NNP
10_1101-436634	34	10	,	,	,
10_1101-436634	34	11	a	a	DT
10_1101-436634	34	12	free	free	JJ
10_1101-436634	34	13	,	,	,
10_1101-436634	34	14	open	open	JJ
10_1101-436634	34	15	-	-	HYPH
10_1101-436634	34	16	source	source	NN
10_1101-436634	34	17	(	(	-LRB-
10_1101-436634	34	18	MIT	MIT	NNP
10_1101-436634	34	19	license	license	NN
10_1101-436634	34	20	)	)	-RRB-
10_1101-436634	34	21	software	software	NN
10_1101-436634	34	22	package	package	NN
10_1101-436634	34	23	that	that	WDT
10_1101-436634	34	24	is	be	VBZ
10_1101-436634	34	25	well	well	RB
10_1101-436634	34	26	-	-	HYPH
10_1101-436634	34	27	documented	document	VBN
10_1101-436634	34	28	,	,	,
10_1101-436634	34	29	modularized	modularize	VBN
10_1101-436634	34	30	for	for	IN
10_1101-436634	34	31	ease	ease	NN
10_1101-436634	34	32	of	of	IN
10_1101-436634	34	33	use	use	NN
10_1101-436634	34	34	,	,	,
10_1101-436634	34	35	and	and	CC
10_1101-436634	34	36	designed	design	VBN
10_1101-436634	34	37	to	to	TO
10_1101-436634	34	38	efficiently	efficiently	RB
10_1101-436634	34	39	identify	identify	VB
10_1101-436634	34	40	potential	potential	JJ
10_1101-436634	34	41	cis	cis	NN
10_1101-436634	34	42	-	-	HYPH
10_1101-436634	34	43	acting	act	VBG
10_1101-436634	34	44	splice	splice	NN
10_1101-436634	34	45	-	-	HYPH
10_1101-436634	34	46	relevant	relevant	JJ
10_1101-436634	34	47	variants	variant	NNS
10_1101-436634	34	48	in	in	IN
10_1101-436634	34	49	tumors	tumor	NNS
10_1101-436634	34	50	(	(	-LRB-
10_1101-436634	34	51	www.regtools.org	www.regtools.org	NNP
10_1101-436634	34	52	)	)	-RRB-
10_1101-436634	34	53	.	.	.
10_1101-436634	35	1	RegTools	RegTools	NNP
10_1101-436634	35	2	is	be	VBZ
10_1101-436634	35	3	a	a	DT
10_1101-436634	35	4	suite	suite	NN
10_1101-436634	35	5	of	of	IN
10_1101-436634	35	6	tools	tool	NNS
10_1101-436634	35	7	designed	design	VBN
10_1101-436634	35	8	to	to	TO
10_1101-436634	35	9	aid	aid	VB
10_1101-436634	35	10	users	user	NNS
10_1101-436634	35	11	in	in	IN
10_1101-436634	35	12	a	a	DT
10_1101-436634	35	13	broad	broad	JJ
10_1101-436634	35	14	range	range	NN
10_1101-436634	35	15	of	of	IN
10_1101-436634	35	16	splicing	splicing	NN
10_1101-436634	35	17	-	-	HYPH
10_1101-436634	35	18	related	relate	VBN
10_1101-436634	35	19	analyses	analysis	NNS
10_1101-436634	35	20	.	.	.
10_1101-436634	36	1	At	at	IN
10_1101-436634	36	2	the	the	DT
10_1101-436634	36	3	highest	high	JJS
10_1101-436634	36	4	level	level	NN
10_1101-436634	36	5	,	,	,
10_1101-436634	36	6	it	-PRON-	PRP
10_1101-436634	36	7	contains	contain	VBZ
10_1101-436634	36	8	three	three	CD
10_1101-436634	36	9	sub	sub	NN
10_1101-436634	36	10	-	-	HYPH
10_1101-436634	36	11	modules	module	NNS
10_1101-436634	36	12	:	:	:
10_1101-436634	36	13	a	a	DT
10_1101-436634	36	14	variants	variant	NNS
10_1101-436634	36	15	module	module	NN
10_1101-436634	36	16	to	to	TO
10_1101-436634	36	17	annotate	annotate	VB
10_1101-436634	36	18	variant	variant	JJ
10_1101-436634	36	19	calls	call	NNS
10_1101-436634	36	20	with	with	IN
10_1101-436634	36	21	respect	respect	NN
10_1101-436634	36	22	to	to	IN
10_1101-436634	36	23	their	-PRON-	PRP$
10_1101-436634	36	24	potential	potential	JJ
10_1101-436634	36	25	splicing	splicing	NN
10_1101-436634	36	26	relevance	relevance	NN
10_1101-436634	36	27	,	,	,
10_1101-436634	36	28	a	a	DT
10_1101-436634	36	29	junctions	junction	NNS
10_1101-436634	36	30	module	module	NN
10_1101-436634	36	31	to	to	TO
10_1101-436634	36	32	analyze	analyze	VB
10_1101-436634	36	33	aligned	align	VBN
10_1101-436634	36	34	RNA	RNA	NNP
10_1101-436634	36	35	-	-	HYPH
10_1101-436634	36	36	seq	seq	NN
10_1101-436634	36	37	data	datum	NNS
10_1101-436634	36	38	and	and	CC
10_1101-436634	36	39	associated	associate	VBD
10_1101-436634	36	40	splicing	splicing	NN
10_1101-436634	36	41	events	event	NNS
10_1101-436634	36	42	,	,	,
10_1101-436634	36	43	and	and	CC
10_1101-436634	36	44	a	a	DT
10_1101-436634	36	45	cis	cis	NN
10_1101-436634	36	46	-	-	HYPH
10_1101-436634	36	47	splice	splice	NN
10_1101-436634	36	48	-	-	HYPH
10_1101-436634	36	49	effects	effect	NNS
10_1101-436634	36	50	module	module	NN
10_1101-436634	36	51	that	that	WDT
10_1101-436634	36	52	integrates	integrate	VBZ
10_1101-436634	36	53	genomic	genomic	JJ
10_1101-436634	36	54	variant	variant	JJ
10_1101-436634	36	55	calls	call	NNS
10_1101-436634	36	56	and	and	CC
10_1101-436634	36	57	transcriptomic	transcriptomic	JJ
10_1101-436634	36	58	sequencing	sequencing	NN
10_1101-436634	36	59	data	datum	NNS
10_1101-436634	36	60	to	to	TO
10_1101-436634	36	61	identify	identify	VB
10_1101-436634	36	62	potential	potential	JJ
10_1101-436634	36	63	splice	splice	NN
10_1101-436634	36	64	-	-	HYPH
10_1101-436634	36	65	altering	alter	VBG
10_1101-436634	36	66	variants	variant	NNS
10_1101-436634	36	67	.	.	.
10_1101-436634	37	1	Each	each	DT
10_1101-436634	37	2	sub	sub	JJ
10_1101-436634	37	3	-	-	HYPH
10_1101-436634	37	4	module	module	NN
10_1101-436634	37	5	contains	contain	VBZ
10_1101-436634	37	6	one	one	CD
10_1101-436634	37	7	or	or	CC
10_1101-436634	37	8	more	more	JJR
10_1101-436634	37	9	commands	command	NNS
10_1101-436634	37	10	,	,	,
10_1101-436634	37	11	which	which	WDT
10_1101-436634	37	12	can	can	MD
10_1101-436634	37	13	be	be	VB
10_1101-436634	37	14	used	use	VBN
10_1101-436634	37	15	individually	individually	RB
10_1101-436634	37	16	or	or	CC
10_1101-436634	37	17	integrated	integrate	VBN
10_1101-436634	37	18	into	into	IN
10_1101-436634	37	19	regulatory	regulatory	JJ
10_1101-436634	37	20	variant	variant	JJ
10_1101-436634	37	21	analysis	analysis	NN
10_1101-436634	37	22	pipelines	pipeline	NNS
10_1101-436634	37	23	.	.	.
10_1101-436634	38	1	To	to	TO
10_1101-436634	38	2	demonstrate	demonstrate	VB
10_1101-436634	38	3	the	the	DT
10_1101-436634	38	4	utility	utility	NN
10_1101-436634	38	5	of	of	IN
10_1101-436634	38	6	RegTools	RegTools	NNP
10_1101-436634	38	7	in	in	IN
10_1101-436634	38	8	identifying	identify	VBG
10_1101-436634	38	9	potential	potential	JJ
10_1101-436634	38	10	splice	splice	NN
10_1101-436634	38	11	-	-	HYPH
10_1101-436634	38	12	relevant	relevant	JJ
10_1101-436634	38	13	variants	variant	NNS
10_1101-436634	38	14	from	from	IN
10_1101-436634	38	15	tumor	tumor	NN
10_1101-436634	38	16	data	datum	NNS
10_1101-436634	38	17	,	,	,
10_1101-436634	38	18	we	-PRON-	PRP
10_1101-436634	38	19	analyzed	analyze	VBD
10_1101-436634	38	20	a	a	DT
10_1101-436634	38	21	combination	combination	NN
10_1101-436634	38	22	of	of	IN
10_1101-436634	38	23	data	datum	NNS
10_1101-436634	38	24	available	available	JJ
10_1101-436634	38	25	from	from	IN
10_1101-436634	38	26	the	the	DT
10_1101-436634	38	27	McDonnell	McDonnell	NNP
10_1101-436634	38	28	Genome	Genome	NNP
10_1101-436634	38	29	Institute	Institute	NNP
10_1101-436634	38	30	(	(	-LRB-
10_1101-436634	38	31	MGI	MGI	NNP
10_1101-436634	38	32	)	)	-RRB-
10_1101-436634	38	33	at	at	IN
10_1101-436634	38	34	Washington	Washington	NNP
10_1101-436634	38	35	University	University	NNP
10_1101-436634	38	36	School	School	NNP
10_1101-436634	38	37	of	of	IN
10_1101-436634	38	38	Medicine	Medicine	NNP
10_1101-436634	38	39	and	and	CC
10_1101-436634	38	40	The	the	DT
10_1101-436634	38	41	Cancer	Cancer	NNP
10_1101-436634	38	42	Genome	Genome	NNP
10_1101-436634	38	43	Atlas	Atlas	NNP
10_1101-436634	38	44	(	(	-LRB-
10_1101-436634	38	45	TCGA	TCGA	NNP
10_1101-436634	38	46	)	)	-RRB-
10_1101-436634	38	47	project	project	NN
10_1101-436634	38	48	.	.	.
10_1101-436634	39	1	In	in	IN
10_1101-436634	39	2	.CC	.CC	NFP
10_1101-436634	39	3	-	-	HYPH
10_1101-436634	39	4	BY	by	IN
10_1101-436634	39	5	-	-	HYPH
10_1101-436634	39	6	NC	NC	NNP
10_1101-436634	39	7	-	-	HYPH
10_1101-436634	39	8	ND	ND	NNP
10_1101-436634	39	9	4.0	4.0	CD
10_1101-436634	39	10	International	international	JJ
10_1101-436634	39	11	licensea	licensea	NNS
10_1101-436634	39	12	certified	certify	VBN
10_1101-436634	39	13	by	by	IN
10_1101-436634	39	14	peer	peer	NN
10_1101-436634	39	15	review	review	NN
10_1101-436634	39	16	)	)	-RRB-
10_1101-436634	39	17	is	be	VBZ
10_1101-436634	39	18	the	the	DT
10_1101-436634	39	19	author	author	NN
10_1101-436634	39	20	/	/	SYM
10_1101-436634	39	21	funder	funder	NN
10_1101-436634	39	22	,	,	,
10_1101-436634	39	23	who	who	WP
10_1101-436634	39	24	has	have	VBZ
10_1101-436634	39	25	granted	grant	VBN
10_1101-436634	39	26	bioRxiv	biorxiv	IN
10_1101-436634	39	27	a	a	DT
10_1101-436634	39	28	license	license	NN
10_1101-436634	39	29	to	to	TO
10_1101-436634	39	30	display	display	VB
10_1101-436634	39	31	the	the	DT
10_1101-436634	39	32	preprint	preprint	NN
10_1101-436634	39	33	in	in	IN
10_1101-436634	39	34	perpetuity	perpetuity	NN
10_1101-436634	39	35	.	.	.
10_1101-436634	40	1	It	-PRON-	PRP
10_1101-436634	40	2	is	be	VBZ
10_1101-436634	40	3	made	make	VBN
10_1101-436634	40	4	available	available	JJ
10_1101-436634	40	5	under	under	IN
10_1101-436634	40	6	The	the	DT
10_1101-436634	40	7	copyright	copyright	NN
10_1101-436634	40	8	holder	holder	NN
10_1101-436634	40	9	for	for	IN
10_1101-436634	40	10	this	this	DT
10_1101-436634	40	11	preprint	preprint	NN
10_1101-436634	40	12	(	(	-LRB-
10_1101-436634	40	13	which	which	WDT
10_1101-436634	40	14	was	be	VBD
10_1101-436634	40	15	notthis	notthis	DT
10_1101-436634	40	16	version	version	NN
10_1101-436634	40	17	posted	post	VBN
10_1101-436634	40	18	January	January	NNP
10_1101-436634	40	19	5	5	CD
10_1101-436634	40	20	,	,	,
10_1101-436634	40	21	2021	2021	CD
10_1101-436634	40	22	.	.	.
10_1101-436634	40	23	;	;	:
10_1101-436634	40	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	40	25	:	:	:
10_1101-436634	40	26	bioRxiv	biorxiv	VB
10_1101-436634	40	27	preprint	preprint	NN
10_1101-436634	40	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	40	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	40	30	3	3	CD
10_1101-436634	40	31	total	total	NN
10_1101-436634	40	32	,	,	,
10_1101-436634	40	33	we	-PRON-	PRP
10_1101-436634	40	34	applied	apply	VBD
10_1101-436634	40	35	RegTools	RegTools	NNP
10_1101-436634	40	36	to	to	IN
10_1101-436634	40	37	9,173	9,173	CD
10_1101-436634	40	38	samples	sample	NNS
10_1101-436634	40	39	across	across	IN
10_1101-436634	40	40	35	35	CD
10_1101-436634	40	41	cancer	cancer	NN
10_1101-436634	40	42	types	type	NNS
10_1101-436634	40	43	.	.	.
10_1101-436634	41	1	We	-PRON-	PRP
10_1101-436634	41	2	contrasted	contrast	VBD
10_1101-436634	41	3	our	-PRON-	PRP$
10_1101-436634	41	4	results	result	NNS
10_1101-436634	41	5	with	with	IN
10_1101-436634	41	6	other	other	JJ
10_1101-436634	41	7	tools	tool	NNS
10_1101-436634	41	8	that	that	WDT
10_1101-436634	41	9	integrate	integrate	VBP
10_1101-436634	41	10	genomic	genomic	JJ
10_1101-436634	41	11	and	and	CC
10_1101-436634	41	12	transcriptomic	transcriptomic	JJ
10_1101-436634	41	13	data	datum	NNS
10_1101-436634	41	14	to	to	TO
10_1101-436634	41	15	identify	identify	VB
10_1101-436634	41	16	potential	potential	JJ
10_1101-436634	41	17	splice	splice	NN
10_1101-436634	41	18	altering	alter	VBG
10_1101-436634	41	19	variants	variant	NNS
10_1101-436634	41	20	,	,	,
10_1101-436634	41	21	specifically	specifically	RB
10_1101-436634	41	22	Veridical	veridical	JJ
10_1101-436634	41	23	,	,	,
10_1101-436634	41	24	MiSplice	MiSplice	NNP
10_1101-436634	41	25	,	,	,
10_1101-436634	41	26	and	and	CC
10_1101-436634	41	27	SAVNet20,21,23	SAVNet20,21,23	NNS
10_1101-436634	41	28	.	.	.
10_1101-436634	42	1	Novel	novel	JJ
10_1101-436634	42	2	junctions	junction	NNS
10_1101-436634	42	3	identified	identify	VBN
10_1101-436634	42	4	by	by	IN
10_1101-436634	42	5	RegTools	regtool	NNS
10_1101-436634	42	6	were	be	VBD
10_1101-436634	42	7	compared	compare	VBN
10_1101-436634	42	8	to	to	IN
10_1101-436634	42	9	data	datum	NNS
10_1101-436634	42	10	from	from	IN
10_1101-436634	42	11	The	the	DT
10_1101-436634	42	12	Genotype	Genotype	NNP
10_1101-436634	42	13	-	-	HYPH
10_1101-436634	42	14	Tissue	Tissue	NNP
10_1101-436634	42	15	Expression	expression	NN
10_1101-436634	42	16	(	(	-LRB-
10_1101-436634	42	17	GTEx	GTEx	NNP
10_1101-436634	42	18	)	)	-RRB-
10_1101-436634	42	19	project	project	NN
10_1101-436634	42	20	to	to	TO
10_1101-436634	42	21	assess	assess	VB
10_1101-436634	42	22	whether	whether	IN
10_1101-436634	42	23	these	these	DT
10_1101-436634	42	24	junctions	junction	NNS
10_1101-436634	42	25	are	be	VBP
10_1101-436634	42	26	present	present	JJ
10_1101-436634	42	27	in	in	IN
10_1101-436634	42	28	normal	normal	JJ
10_1101-436634	42	29	tissues24	tissues24	NNS
10_1101-436634	42	30	.	.	.
10_1101-436634	43	1	Variants	variant	NNS
10_1101-436634	43	2	significantly	significantly	RB
10_1101-436634	43	3	associated	associate	VBN
10_1101-436634	43	4	with	with	IN
10_1101-436634	43	5	novel	novel	JJ
10_1101-436634	43	6	junctions	junction	NNS
10_1101-436634	43	7	were	be	VBD
10_1101-436634	43	8	processed	process	VBN
10_1101-436634	43	9	through	through	IN
10_1101-436634	43	10	VEP	VEP	NNP
10_1101-436634	43	11	and	and	CC
10_1101-436634	43	12	Illumina	Illumina	NNP
10_1101-436634	43	13	’s	’s	POS
10_1101-436634	43	14	SpliceAI	SpliceAI	VBN
10_1101-436634	43	15	tool	tool	NN
10_1101-436634	43	16	to	to	TO
10_1101-436634	43	17	compare	compare	VB
10_1101-436634	43	18	our	-PRON-	PRP$
10_1101-436634	43	19	findings	finding	NNS
10_1101-436634	43	20	with	with	IN
10_1101-436634	43	21	splicing	splicing	NN
10_1101-436634	43	22	consequences	consequence	NNS
10_1101-436634	43	23	predicted	predict	VBD
10_1101-436634	43	24	based	base	VBN
10_1101-436634	43	25	on	on	IN
10_1101-436634	43	26	the	the	DT
10_1101-436634	43	27	variant	variant	JJ
10_1101-436634	43	28	information	information	NN
10_1101-436634	43	29	alone13,25	alone13,25	NNP
10_1101-436634	43	30	.	.	.
10_1101-436634	44	1	With	with	IN
10_1101-436634	44	2	this	this	DT
10_1101-436634	44	3	additional	additional	JJ
10_1101-436634	44	4	analysis	analysis	NN
10_1101-436634	44	5	,	,	,
10_1101-436634	44	6	we	-PRON-	PRP
10_1101-436634	44	7	were	be	VBD
10_1101-436634	44	8	able	able	JJ
10_1101-436634	44	9	to	to	TO
10_1101-436634	44	10	more	more	RBR
10_1101-436634	44	11	easily	easily	RB
10_1101-436634	44	12	identify	identify	VB
10_1101-436634	44	13	both	both	DT
10_1101-436634	44	14	variants	variant	NNS
10_1101-436634	44	15	in	in	IN
10_1101-436634	44	16	known	know	VBN
10_1101-436634	44	17	cancer	cancer	NN
10_1101-436634	44	18	drivers	driver	NNS
10_1101-436634	44	19	,	,	,
10_1101-436634	44	20	whose	whose	WP$
10_1101-436634	44	21	splicing	splicing	NN
10_1101-436634	44	22	consequences	consequence	NNS
10_1101-436634	44	23	have	have	VBP
10_1101-436634	44	24	not	not	RB
10_1101-436634	44	25	been	be	VBN
10_1101-436634	44	26	previously	previously	RB
10_1101-436634	44	27	reported	report	VBN
10_1101-436634	44	28	in	in	IN
10_1101-436634	44	29	the	the	DT
10_1101-436634	44	30	literature	literature	NN
10_1101-436634	44	31	,	,	,
10_1101-436634	44	32	and	and	CC
10_1101-436634	44	33	potentially	potentially	RB
10_1101-436634	44	34	novel	novel	JJ
10_1101-436634	44	35	cancer	cancer	NN
10_1101-436634	44	36	drivers	driver	NNS
10_1101-436634	44	37	,	,	,
10_1101-436634	44	38	whose	whose	WP$
10_1101-436634	44	39	disruption	disruption	NN
10_1101-436634	44	40	relies	rely	VBZ
10_1101-436634	44	41	on	on	IN
10_1101-436634	44	42	splice	splice	NN
10_1101-436634	44	43	-	-	HYPH
10_1101-436634	44	44	altering	alter	VBG
10_1101-436634	44	45	mutations	mutation	NNS
10_1101-436634	44	46	Results	result	NNS
10_1101-436634	44	47	The	the	DT
10_1101-436634	44	48	RegTools	RegTools	NNP
10_1101-436634	44	49	tool	tool	NN
10_1101-436634	44	50	suite	suite	NN
10_1101-436634	44	51	supports	support	NNS
10_1101-436634	44	52	splice	splice	NN
10_1101-436634	44	53	regulatory	regulatory	JJ
10_1101-436634	44	54	variant	variant	JJ
10_1101-436634	44	55	discovery	discovery	NN
10_1101-436634	44	56	by	by	IN
10_1101-436634	44	57	the	the	DT
10_1101-436634	44	58	integration	integration	NN
10_1101-436634	44	59	of	of	IN
10_1101-436634	44	60	genome	genome	NN
10_1101-436634	44	61	and	and	CC
10_1101-436634	44	62	transcriptome	transcriptome	DT
10_1101-436634	44	63	data	datum	NNS
10_1101-436634	44	64	.	.	.
10_1101-436634	45	1	RegTools	RegTools	NNP
10_1101-436634	45	2	is	be	VBZ
10_1101-436634	45	3	a	a	DT
10_1101-436634	45	4	suite	suite	NN
10_1101-436634	45	5	of	of	IN
10_1101-436634	45	6	tools	tool	NNS
10_1101-436634	45	7	designed	design	VBN
10_1101-436634	45	8	to	to	TO
10_1101-436634	45	9	aid	aid	VB
10_1101-436634	45	10	users	user	NNS
10_1101-436634	45	11	in	in	IN
10_1101-436634	45	12	a	a	DT
10_1101-436634	45	13	broad	broad	JJ
10_1101-436634	45	14	range	range	NN
10_1101-436634	45	15	of	of	IN
10_1101-436634	45	16	splicing	splicing	NN
10_1101-436634	45	17	-	-	HYPH
10_1101-436634	45	18	related	relate	VBN
10_1101-436634	45	19	analyses	analysis	NNS
10_1101-436634	45	20	.	.	.
10_1101-436634	46	1	The	the	DT
10_1101-436634	46	2	variants	variant	NNS
10_1101-436634	46	3	module	module	NN
10_1101-436634	46	4	contains	contain	VBZ
10_1101-436634	46	5	the	the	DT
10_1101-436634	46	6	annotate	annotate	JJ
10_1101-436634	46	7	command	command	NN
10_1101-436634	46	8	.	.	.
10_1101-436634	47	1	The	the	DT
10_1101-436634	47	2	variants	variant	NNS
10_1101-436634	47	3	annotate	annotate	VBP
10_1101-436634	47	4	command	command	NN
10_1101-436634	47	5	takes	take	VBZ
10_1101-436634	47	6	a	a	DT
10_1101-436634	47	7	VCF	VCF	NNP
10_1101-436634	47	8	of	of	IN
10_1101-436634	47	9	somatic	somatic	JJ
10_1101-436634	47	10	variant	variant	JJ
10_1101-436634	47	11	calls	call	NNS
10_1101-436634	47	12	and	and	CC
10_1101-436634	47	13	a	a	DT
10_1101-436634	47	14	GTF	gtf	NN
10_1101-436634	47	15	of	of	IN
10_1101-436634	47	16	transcriptome	transcriptome	DT
10_1101-436634	47	17	annotations	annotation	NNS
10_1101-436634	47	18	as	as	IN
10_1101-436634	47	19	input	input	NN
10_1101-436634	47	20	.	.	.
10_1101-436634	48	1	RegTools	RegTools	NNP
10_1101-436634	48	2	does	do	VBZ
10_1101-436634	48	3	not	not	RB
10_1101-436634	48	4	have	have	VB
10_1101-436634	48	5	any	any	DT
10_1101-436634	48	6	particular	particular	JJ
10_1101-436634	48	7	preference	preference	NN
10_1101-436634	48	8	for	for	IN
10_1101-436634	48	9	variant	variant	JJ
10_1101-436634	48	10	callers	caller	NNS
10_1101-436634	48	11	or	or	CC
10_1101-436634	48	12	reference	reference	NN
10_1101-436634	48	13	annotations	annotation	NNS
10_1101-436634	48	14	.	.	.
10_1101-436634	49	1	Each	each	DT
10_1101-436634	49	2	variant	variant	NN
10_1101-436634	49	3	is	be	VBZ
10_1101-436634	49	4	annotated	annotate	VBN
10_1101-436634	49	5	by	by	IN
10_1101-436634	49	6	RegTools	RegTools	NNP
10_1101-436634	49	7	with	with	IN
10_1101-436634	49	8	known	know	VBN
10_1101-436634	49	9	overlapping	overlap	VBG
10_1101-436634	49	10	genes	gene	NNS
10_1101-436634	49	11	and	and	CC
10_1101-436634	49	12	transcripts	transcript	NNS
10_1101-436634	49	13	,	,	,
10_1101-436634	49	14	and	and	CC
10_1101-436634	49	15	is	be	VBZ
10_1101-436634	49	16	categorized	categorize	VBN
10_1101-436634	49	17	into	into	IN
10_1101-436634	49	18	one	one	CD
10_1101-436634	49	19	of	of	IN
10_1101-436634	49	20	several	several	JJ
10_1101-436634	49	21	user	user	NN
10_1101-436634	49	22	-	-	HYPH
10_1101-436634	49	23	configurable	configurable	JJ
10_1101-436634	49	24	“	"	``
10_1101-436634	49	25	variant	variant	JJ
10_1101-436634	49	26	types	type	NNS
10_1101-436634	49	27	”	"	''
10_1101-436634	49	28	,	,	,
10_1101-436634	49	29	based	base	VBN
10_1101-436634	49	30	on	on	IN
10_1101-436634	49	31	position	position	NN
10_1101-436634	49	32	relative	relative	JJ
10_1101-436634	49	33	to	to	IN
10_1101-436634	49	34	the	the	DT
10_1101-436634	49	35	edges	edge	NNS
10_1101-436634	49	36	of	of	IN
10_1101-436634	49	37	known	know	VBN
10_1101-436634	49	38	exons	exon	NNS
10_1101-436634	49	39	.	.	.
10_1101-436634	50	1	The	the	DT
10_1101-436634	50	2	variant	variant	JJ
10_1101-436634	50	3	type	type	NN
10_1101-436634	50	4	annotation	annotation	NN
10_1101-436634	50	5	depends	depend	VBZ
10_1101-436634	50	6	on	on	IN
10_1101-436634	50	7	the	the	DT
10_1101-436634	50	8	stringency	stringency	NN
10_1101-436634	50	9	for	for	IN
10_1101-436634	50	10	splicing	splicing	NN
10_1101-436634	50	11	-	-	HYPH
10_1101-436634	50	12	relevance	relevance	NN
10_1101-436634	50	13	that	that	IN
10_1101-436634	50	14	the	the	DT
10_1101-436634	50	15	user	user	NN
10_1101-436634	50	16	sets	set	VBZ
10_1101-436634	50	17	with	with	IN
10_1101-436634	50	18	the	the	DT
10_1101-436634	50	19	“	"	``
10_1101-436634	50	20	splice	splice	NN
10_1101-436634	50	21	variant	variant	JJ
10_1101-436634	50	22	window	window	NN
10_1101-436634	50	23	”	"	''
10_1101-436634	50	24	setting	setting	NN
10_1101-436634	50	25	.	.	.
10_1101-436634	51	1	By	by	IN
10_1101-436634	51	2	default	default	NN
10_1101-436634	51	3	,	,	,
10_1101-436634	51	4	RegTools	RegTools	NNP
10_1101-436634	51	5	marks	mark	VBZ
10_1101-436634	51	6	intronic	intronic	JJ
10_1101-436634	51	7	variants	variant	NNS
10_1101-436634	51	8	within	within	IN
10_1101-436634	51	9	2	2	CD
10_1101-436634	51	10	bp	bp	NN
10_1101-436634	51	11	of	of	IN
10_1101-436634	51	12	the	the	DT
10_1101-436634	51	13	exon	exon	JJ
10_1101-436634	51	14	edge	edge	NN
10_1101-436634	51	15	as	as	IN
10_1101-436634	51	16	“	"	``
10_1101-436634	51	17	splicing	splice	VBG
10_1101-436634	51	18	intronic	intronic	JJ
10_1101-436634	51	19	”	"	''
10_1101-436634	51	20	,	,	,
10_1101-436634	51	21	exonic	exonic	JJ
10_1101-436634	51	22	variants	variant	NNS
10_1101-436634	51	23	within	within	IN
10_1101-436634	51	24	3	3	CD
10_1101-436634	51	25	bp	bp	NN
10_1101-436634	51	26	as	as	IN
10_1101-436634	51	27	“	"	``
10_1101-436634	51	28	splicing	splice	VBG
10_1101-436634	51	29	exonic	exonic	JJ
10_1101-436634	51	30	”	"	''
10_1101-436634	51	31	,	,	,
10_1101-436634	51	32	other	other	JJ
10_1101-436634	51	33	intronic	intronic	JJ
10_1101-436634	51	34	variants	variant	NNS
10_1101-436634	51	35	as	as	IN
10_1101-436634	51	36	“	"	``
10_1101-436634	51	37	intronic	intronic	JJ
10_1101-436634	51	38	”	"	''
10_1101-436634	51	39	,	,	,
10_1101-436634	51	40	and	and	CC
10_1101-436634	51	41	other	other	JJ
10_1101-436634	51	42	exonic	exonic	JJ
10_1101-436634	51	43	variants	variant	NNS
10_1101-436634	51	44	simply	simply	RB
10_1101-436634	51	45	as	as	IN
10_1101-436634	51	46	“	"	``
10_1101-436634	51	47	exonic	exonic	JJ
10_1101-436634	51	48	.	.	.
10_1101-436634	51	49	”	"	''
10_1101-436634	51	50	RegTools	RegTools	NNP
10_1101-436634	51	51	considers	consider	VBZ
10_1101-436634	51	52	only	only	RB
10_1101-436634	51	53	“	"	``
10_1101-436634	51	54	splicing	splice	VBG
10_1101-436634	51	55	intronic	intronic	JJ
10_1101-436634	51	56	”	"	''
10_1101-436634	51	57	and	and	CC
10_1101-436634	51	58	“	"	``
10_1101-436634	51	59	splicing	splice	VBG
10_1101-436634	51	60	exonic	exonic	JJ
10_1101-436634	51	61	”	"	''
10_1101-436634	51	62	as	as	IN
10_1101-436634	51	63	important	important	JJ
10_1101-436634	51	64	.	.	.
10_1101-436634	52	1	To	to	TO
10_1101-436634	52	2	allow	allow	VB
10_1101-436634	52	3	for	for	IN
10_1101-436634	52	4	discovery	discovery	NN
10_1101-436634	52	5	of	of	IN
10_1101-436634	52	6	an	an	DT
10_1101-436634	52	7	arbitrarily	arbitrarily	RB
10_1101-436634	52	8	expansive	expansive	JJ
10_1101-436634	52	9	set	set	NN
10_1101-436634	52	10	of	of	IN
10_1101-436634	52	11	variants	variant	NNS
10_1101-436634	52	12	,	,	,
10_1101-436634	52	13	RegTools	RegTools	NNP
10_1101-436634	52	14	allows	allow	VBZ
10_1101-436634	52	15	the	the	DT
10_1101-436634	52	16	user	user	NN
10_1101-436634	52	17	to	to	TO
10_1101-436634	52	18	customize	customize	VB
10_1101-436634	52	19	the	the	DT
10_1101-436634	52	20	size	size	NN
10_1101-436634	52	21	of	of	IN
10_1101-436634	52	22	the	the	DT
10_1101-436634	52	23	exonic	exonic	JJ
10_1101-436634	52	24	/	/	SYM
10_1101-436634	52	25	intronic	intronic	JJ
10_1101-436634	52	26	windows	window	NNS
10_1101-436634	52	27	individually	individually	RB
10_1101-436634	52	28	(	(	-LRB-
10_1101-436634	52	29	e.g.	e.g.	RB
10_1101-436634	53	1	-i	-i	:
10_1101-436634	53	2	50	50	CD
10_1101-436634	53	3	-e	-e	SYM
10_1101-436634	53	4	5	5	CD
10_1101-436634	53	5	for	for	IN
10_1101-436634	53	6	intronic	intronic	JJ
10_1101-436634	53	7	variants	variant	NNS
10_1101-436634	53	8	50	50	CD
10_1101-436634	53	9	bp	bp	NN
10_1101-436634	53	10	from	from	IN
10_1101-436634	53	11	an	an	DT
10_1101-436634	53	12	exon	exon	JJ
10_1101-436634	53	13	edge	edge	NN
10_1101-436634	53	14	and	and	CC
10_1101-436634	53	15	exonic	exonic	JJ
10_1101-436634	53	16	variants	variant	NNS
10_1101-436634	53	17	5	5	CD
10_1101-436634	53	18	bp	bp	NN
10_1101-436634	53	19	from	from	IN
10_1101-436634	53	20	an	an	DT
10_1101-436634	53	21	exon	exon	JJ
10_1101-436634	53	22	edge	edge	NN
10_1101-436634	53	23	)	)	-RRB-
10_1101-436634	53	24	or	or	CC
10_1101-436634	53	25	even	even	RB
10_1101-436634	53	26	consider	consider	VB
10_1101-436634	53	27	all	all	RB
10_1101-436634	53	28	exonic	exonic	JJ
10_1101-436634	53	29	/	/	SYM
10_1101-436634	53	30	intronic	intronic	JJ
10_1101-436634	53	31	variants	variant	NNS
10_1101-436634	53	32	as	as	IN
10_1101-436634	53	33	potentially	potentially	RB
10_1101-436634	53	34	splicing	splice	VBG
10_1101-436634	53	35	-	-	HYPH
10_1101-436634	53	36	relevant	relevant	JJ
10_1101-436634	53	37	(	(	-LRB-
10_1101-436634	53	38	e.g.	e.g.	RB
10_1101-436634	54	1	-E	-E	:
10_1101-436634	54	2	or	or	CC
10_1101-436634	54	3	-I	-I	.
10_1101-436634	54	4	)	)	-RRB-
10_1101-436634	54	5	(	(	-LRB-
10_1101-436634	54	6	Figure	figure	NN
10_1101-436634	54	7	1A	1a	NN
10_1101-436634	54	8	)	)	-RRB-
10_1101-436634	54	9	.	.	.
10_1101-436634	55	1	The	the	DT
10_1101-436634	55	2	junctions	junction	NNS
10_1101-436634	55	3	module	module	NN
10_1101-436634	55	4	contains	contain	VBZ
10_1101-436634	55	5	the	the	DT
10_1101-436634	55	6	extract	extract	NN
10_1101-436634	55	7	and	and	CC
10_1101-436634	55	8	annotate	annotate	JJ
10_1101-436634	55	9	commands	command	NNS
10_1101-436634	55	10	.	.	.
10_1101-436634	56	1	The	the	DT
10_1101-436634	56	2	junctions	junction	NNS
10_1101-436634	56	3	extract	extract	VBP
10_1101-436634	56	4	command	command	NN
10_1101-436634	56	5	takes	take	VBZ
10_1101-436634	56	6	an	an	DT
10_1101-436634	56	7	alignment	alignment	NN
10_1101-436634	56	8	file	file	NN
10_1101-436634	56	9	containing	contain	VBG
10_1101-436634	56	10	aligned	align	VBN
10_1101-436634	56	11	RNA	RNA	NNP
10_1101-436634	56	12	-	-	HYPH
10_1101-436634	56	13	seq	seq	NN
10_1101-436634	56	14	reads	read	NNS
10_1101-436634	56	15	,	,	,
10_1101-436634	56	16	infers	infer	VBZ
10_1101-436634	56	17	the	the	DT
10_1101-436634	56	18	exon	exon	NN
10_1101-436634	56	19	-	-	HYPH
10_1101-436634	56	20	exon	exon	NN
10_1101-436634	56	21	boundaries	boundary	NNS
10_1101-436634	56	22	based	base	VBN
10_1101-436634	56	23	on	on	IN
10_1101-436634	56	24	the	the	DT
10_1101-436634	56	25	CIGAR	cigar	NN
10_1101-436634	56	26	strings26	strings26	NN
10_1101-436634	56	27	,	,	,
10_1101-436634	56	28	and	and	CC
10_1101-436634	56	29	outputs	output	NNS
10_1101-436634	56	30	each	each	DT
10_1101-436634	56	31	“	"	``
10_1101-436634	56	32	junction	junction	NN
10_1101-436634	56	33	”	"	''
10_1101-436634	56	34	as	as	IN
10_1101-436634	56	35	a	a	DT
10_1101-436634	56	36	feature	feature	NN
10_1101-436634	56	37	in	in	IN
10_1101-436634	56	38	BED12	BED12	NNP
10_1101-436634	56	39	format	format	NN
10_1101-436634	56	40	.	.	.
10_1101-436634	57	1	The	the	DT
10_1101-436634	57	2	junctions	junction	NNS
10_1101-436634	57	3	annotate	annotate	VBP
10_1101-436634	57	4	command	command	NN
10_1101-436634	57	5	takes	take	VBZ
10_1101-436634	57	6	a	a	DT
10_1101-436634	57	7	file	file	NN
10_1101-436634	57	8	of	of	IN
10_1101-436634	57	9	junctions	junction	NNS
10_1101-436634	57	10	in	in	IN
10_1101-436634	57	11	BED12	BED12	NNP
10_1101-436634	57	12	format	format	NN
10_1101-436634	57	13	(	(	-LRB-
10_1101-436634	57	14	such	such	JJ
10_1101-436634	57	15	as	as	IN
10_1101-436634	57	16	the	the	DT
10_1101-436634	57	17	one	one	CD
10_1101-436634	57	18	output	output	NN
10_1101-436634	57	19	by	by	IN
10_1101-436634	57	20	junctions	junction	NNS
10_1101-436634	57	21	extract	extract	NNP
10_1101-436634	57	22	)	)	-RRB-
10_1101-436634	57	23	,	,	,
10_1101-436634	57	24	a	a	DT
10_1101-436634	57	25	FASTA	FASTA	NNP
10_1101-436634	57	26	file	file	NN
10_1101-436634	57	27	containing	contain	VBG
10_1101-436634	57	28	the	the	DT
10_1101-436634	57	29	reference	reference	NN
10_1101-436634	57	30	genome	genome	NN
10_1101-436634	57	31	,	,	,
10_1101-436634	57	32	and	and	CC
10_1101-436634	57	33	a	a	DT
10_1101-436634	57	34	GTF	gtf	NN
10_1101-436634	57	35	file	file	NN
10_1101-436634	57	36	containing	contain	VBG
10_1101-436634	57	37	reference	reference	NN
10_1101-436634	57	38	transcriptome	transcriptome	DT
10_1101-436634	57	39	annotations	annotation	NNS
10_1101-436634	57	40	and	and	CC
10_1101-436634	57	41	generates	generate	VBZ
10_1101-436634	57	42	a	a	DT
10_1101-436634	57	43	TSV	TSV	NNP
10_1101-436634	57	44	file	file	NN
10_1101-436634	57	45	,	,	,
10_1101-436634	57	46	annotating	annotate	VBG
10_1101-436634	57	47	each	each	DT
10_1101-436634	57	48	junction	junction	NN
10_1101-436634	57	49	with	with	IN
10_1101-436634	57	50	:	:	:
10_1101-436634	57	51	the	the	DT
10_1101-436634	57	52	number	number	NN
10_1101-436634	57	53	of	of	IN
10_1101-436634	57	54	acceptor	acceptor	NN
10_1101-436634	57	55	sites	site	NNS
10_1101-436634	57	56	,	,	,
10_1101-436634	57	57	donor	donor	NN
10_1101-436634	57	58	sites	site	NNS
10_1101-436634	57	59	,	,	,
10_1101-436634	57	60	and	and	CC
10_1101-436634	57	61	exons	exon	NNS
10_1101-436634	57	62	skipped	skip	VBD
10_1101-436634	57	63	,	,	,
10_1101-436634	57	64	and	and	CC
10_1101-436634	57	65	the	the	DT
10_1101-436634	57	66	identities	identity	NNS
10_1101-436634	57	67	of	of	IN
10_1101-436634	57	68	known	know	VBN
10_1101-436634	57	69	overlapping	overlap	VBG
10_1101-436634	57	70	transcripts	transcript	NNS
10_1101-436634	57	71	and	and	CC
10_1101-436634	57	72	genes	gene	NNS
10_1101-436634	57	73	.	.	.
10_1101-436634	58	1	We	-PRON-	PRP
10_1101-436634	58	2	also	also	RB
10_1101-436634	58	3	annotate	annotate	VBP
10_1101-436634	58	4	the	the	DT
10_1101-436634	58	5	“	"	``
10_1101-436634	58	6	junction	junction	NN
10_1101-436634	58	7	type	type	NN
10_1101-436634	58	8	”	"	''
10_1101-436634	58	9	,	,	,
10_1101-436634	58	10	which	which	WDT
10_1101-436634	58	11	denotes	denote	VBZ
10_1101-436634	58	12	if	if	IN
10_1101-436634	58	13	and	and	CC
10_1101-436634	58	14	how	how	WRB
10_1101-436634	58	15	the	the	DT
10_1101-436634	58	16	junction	junction	NN
10_1101-436634	58	17	is	be	VBZ
10_1101-436634	58	18	novel	novel	JJ
10_1101-436634	58	19	(	(	-LRB-
10_1101-436634	58	20	i.e.	i.e.	FW
10_1101-436634	59	1	different	different	JJ
10_1101-436634	59	2	compared	compare	VBN
10_1101-436634	59	3	to	to	IN
10_1101-436634	59	4	provided	provide	VBN
10_1101-436634	59	5	transcript	transcript	NN
10_1101-436634	59	6	annotations	annotation	NNS
10_1101-436634	59	7	)	)	-RRB-
10_1101-436634	59	8	.	.	.
10_1101-436634	60	1	If	if	IN
10_1101-436634	60	2	the	the	DT
10_1101-436634	60	3	donor	donor	NN
10_1101-436634	60	4	is	be	VBZ
10_1101-436634	60	5	known	know	VBN
10_1101-436634	60	6	,	,	,
10_1101-436634	60	7	but	but	CC
10_1101-436634	60	8	the	the	DT
10_1101-436634	60	9	acceptor	acceptor	NN
10_1101-436634	60	10	is	be	VBZ
10_1101-436634	60	11	not	not	RB
10_1101-436634	60	12	or	or	CC
10_1101-436634	60	13	vice	vice	RB
10_1101-436634	60	14	-	-	HYPH
10_1101-436634	60	15	versa	versa	JJ
10_1101-436634	60	16	,	,	,
10_1101-436634	60	17	it	-PRON-	PRP
10_1101-436634	60	18	is	be	VBZ
10_1101-436634	60	19	marked	mark	VBN
10_1101-436634	60	20	as	as	IN
10_1101-436634	60	21	“	"	``
10_1101-436634	60	22	D	d	NN
10_1101-436634	60	23	”	"	''
10_1101-436634	60	24	or	or	CC
10_1101-436634	60	25	“	"	``
10_1101-436634	60	26	A	a	NN
10_1101-436634	60	27	”	"	''
10_1101-436634	60	28	,	,	,
10_1101-436634	60	29	respectively	respectively	RB
10_1101-436634	60	30	.	.	.
10_1101-436634	61	1	If	if	IN
10_1101-436634	61	2	both	both	DT
10_1101-436634	61	3	are	be	VBP
10_1101-436634	61	4	known	know	VBN
10_1101-436634	61	5	,	,	,
10_1101-436634	61	6	but	but	CC
10_1101-436634	61	7	the	the	DT
10_1101-436634	61	8	pairing	pairing	NN
10_1101-436634	61	9	is	be	VBZ
10_1101-436634	61	10	not	not	RB
10_1101-436634	61	11	known	know	VBN
10_1101-436634	61	12	,	,	,
10_1101-436634	61	13	it	-PRON-	PRP
10_1101-436634	61	14	is	be	VBZ
10_1101-436634	61	15	marked	mark	VBN
10_1101-436634	61	16	as	as	IN
10_1101-436634	61	17	“	"	``
10_1101-436634	61	18	NDA	NDA	NNP
10_1101-436634	61	19	”	"	''
10_1101-436634	61	20	,	,	,
10_1101-436634	61	21	whereas	whereas	IN
10_1101-436634	61	22	if	if	IN
10_1101-436634	61	23	both	both	DT
10_1101-436634	61	24	are	be	VBP
10_1101-436634	61	25	.CC	.CC	:
10_1101-436634	61	26	-	-	:
10_1101-436634	61	27	BY	by	IN
10_1101-436634	61	28	-	-	HYPH
10_1101-436634	61	29	NC	NC	NNP
10_1101-436634	61	30	-	-	HYPH
10_1101-436634	61	31	ND	ND	NNP
10_1101-436634	61	32	4.0	4.0	CD
10_1101-436634	61	33	International	international	JJ
10_1101-436634	61	34	licensea	licensea	NNS
10_1101-436634	61	35	certified	certify	VBN
10_1101-436634	61	36	by	by	IN
10_1101-436634	61	37	peer	peer	NN
10_1101-436634	61	38	review	review	NN
10_1101-436634	61	39	)	)	-RRB-
10_1101-436634	61	40	is	be	VBZ
10_1101-436634	61	41	the	the	DT
10_1101-436634	61	42	author	author	NN
10_1101-436634	61	43	/	/	SYM
10_1101-436634	61	44	funder	funder	NN
10_1101-436634	61	45	,	,	,
10_1101-436634	61	46	who	who	WP
10_1101-436634	61	47	has	have	VBZ
10_1101-436634	61	48	granted	grant	VBN
10_1101-436634	61	49	bioRxiv	biorxiv	IN
10_1101-436634	61	50	a	a	DT
10_1101-436634	61	51	license	license	NN
10_1101-436634	61	52	to	to	TO
10_1101-436634	61	53	display	display	VB
10_1101-436634	61	54	the	the	DT
10_1101-436634	61	55	preprint	preprint	NN
10_1101-436634	61	56	in	in	IN
10_1101-436634	61	57	perpetuity	perpetuity	NN
10_1101-436634	61	58	.	.	.
10_1101-436634	62	1	It	-PRON-	PRP
10_1101-436634	62	2	is	be	VBZ
10_1101-436634	62	3	made	make	VBN
10_1101-436634	62	4	available	available	JJ
10_1101-436634	62	5	under	under	IN
10_1101-436634	62	6	The	the	DT
10_1101-436634	62	7	copyright	copyright	NN
10_1101-436634	62	8	holder	holder	NN
10_1101-436634	62	9	for	for	IN
10_1101-436634	62	10	this	this	DT
10_1101-436634	62	11	preprint	preprint	NN
10_1101-436634	62	12	(	(	-LRB-
10_1101-436634	62	13	which	which	WDT
10_1101-436634	62	14	was	be	VBD
10_1101-436634	62	15	notthis	notthis	DT
10_1101-436634	62	16	version	version	NN
10_1101-436634	62	17	posted	post	VBN
10_1101-436634	62	18	January	January	NNP
10_1101-436634	62	19	5	5	CD
10_1101-436634	62	20	,	,	,
10_1101-436634	62	21	2021	2021	CD
10_1101-436634	62	22	.	.	.
10_1101-436634	62	23	;	;	:
10_1101-436634	62	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	62	25	:	:	:
10_1101-436634	62	26	bioRxiv	biorxiv	VB
10_1101-436634	62	27	preprint	preprint	NN
10_1101-436634	62	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	62	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	62	30	4	4	CD
10_1101-436634	62	31	unknown	unknown	JJ
10_1101-436634	62	32	,	,	,
10_1101-436634	62	33	it	-PRON-	PRP
10_1101-436634	62	34	is	be	VBZ
10_1101-436634	62	35	marked	mark	VBN
10_1101-436634	62	36	as	as	IN
10_1101-436634	62	37	“	"	``
10_1101-436634	62	38	N	N	NNP
10_1101-436634	62	39	”	"	''
10_1101-436634	62	40	.	.	.
10_1101-436634	63	1	If	if	IN
10_1101-436634	63	2	the	the	DT
10_1101-436634	63	3	junction	junction	NN
10_1101-436634	63	4	is	be	VBZ
10_1101-436634	63	5	not	not	RB
10_1101-436634	63	6	novel	novel	JJ
10_1101-436634	63	7	(	(	-LRB-
10_1101-436634	63	8	i.e.	i.e.	FW
10_1101-436634	64	1	it	-PRON-	PRP
10_1101-436634	64	2	appears	appear	VBZ
10_1101-436634	64	3	in	in	IN
10_1101-436634	64	4	at	at	RB
10_1101-436634	64	5	least	least	RBS
10_1101-436634	64	6	one	one	CD
10_1101-436634	64	7	transcript	transcript	NN
10_1101-436634	64	8	in	in	IN
10_1101-436634	64	9	the	the	DT
10_1101-436634	64	10	supplied	supplied	JJ
10_1101-436634	64	11	GTF	GTF	NNP
10_1101-436634	64	12	)	)	-RRB-
10_1101-436634	64	13	,	,	,
10_1101-436634	64	14	it	-PRON-	PRP
10_1101-436634	64	15	is	be	VBZ
10_1101-436634	64	16	marked	mark	VBN
10_1101-436634	64	17	as	as	IN
10_1101-436634	64	18	“	"	``
10_1101-436634	64	19	DA	DA	NNP
10_1101-436634	64	20	”	"	''
10_1101-436634	64	21	(	(	-LRB-
10_1101-436634	64	22	Figure	figure	NN
10_1101-436634	64	23	1B	1b	NN
10_1101-436634	64	24	)	)	-RRB-
10_1101-436634	64	25	.	.	.
10_1101-436634	65	1	The	the	DT
10_1101-436634	65	2	cis	cis	NN
10_1101-436634	65	3	-	-	HYPH
10_1101-436634	65	4	splice	splice	NN
10_1101-436634	65	5	-	-	HYPH
10_1101-436634	65	6	effects	effect	NNS
10_1101-436634	65	7	module	module	NN
10_1101-436634	65	8	contains	contain	VBZ
10_1101-436634	65	9	the	the	DT
10_1101-436634	65	10	identify	identify	NN
10_1101-436634	65	11	command	command	NN
10_1101-436634	65	12	,	,	,
10_1101-436634	65	13	which	which	WDT
10_1101-436634	65	14	identifies	identify	VBZ
10_1101-436634	65	15	potential	potential	JJ
10_1101-436634	65	16	splice-	splice-	NNP
10_1101-436634	65	17	altering	alter	VBG
10_1101-436634	65	18	variants	variant	NNS
10_1101-436634	65	19	from	from	IN
10_1101-436634	65	20	sequencing	sequence	VBG
10_1101-436634	65	21	data	datum	NNS
10_1101-436634	65	22	.	.	.
10_1101-436634	66	1	The	the	DT
10_1101-436634	66	2	following	follow	VBG
10_1101-436634	66	3	are	be	VBP
10_1101-436634	66	4	required	require	VBN
10_1101-436634	66	5	as	as	IN
10_1101-436634	66	6	input	input	NN
10_1101-436634	66	7	:	:	:
10_1101-436634	66	8	a	a	DT
10_1101-436634	66	9	VCF	VCF	NNP
10_1101-436634	66	10	file	file	NN
10_1101-436634	66	11	containing	contain	VBG
10_1101-436634	66	12	variant	variant	JJ
10_1101-436634	66	13	calls	call	NNS
10_1101-436634	66	14	,	,	,
10_1101-436634	66	15	an	an	DT
10_1101-436634	66	16	alignment	alignment	NN
10_1101-436634	66	17	file	file	NN
10_1101-436634	66	18	containing	contain	VBG
10_1101-436634	66	19	aligned	align	VBN
10_1101-436634	66	20	RNA	RNA	NNP
10_1101-436634	66	21	-	-	HYPH
10_1101-436634	66	22	sequencing	sequence	VBG
10_1101-436634	66	23	reads	read	NNS
10_1101-436634	66	24	,	,	,
10_1101-436634	66	25	a	a	DT
10_1101-436634	66	26	reference	reference	NN
10_1101-436634	66	27	genome	genome	JJ
10_1101-436634	66	28	FASTA	FASTA	NNP
10_1101-436634	66	29	file	file	NN
10_1101-436634	66	30	,	,	,
10_1101-436634	66	31	and	and	CC
10_1101-436634	66	32	a	a	DT
10_1101-436634	66	33	reference	reference	NN
10_1101-436634	66	34	transcriptome	transcriptome	DT
10_1101-436634	66	35	GTF	gtf	NN
10_1101-436634	66	36	file	file	NN
10_1101-436634	66	37	.	.	.
10_1101-436634	67	1	The	the	DT
10_1101-436634	67	2	identify	identify	NN
10_1101-436634	67	3	pipeline	pipeline	NN
10_1101-436634	67	4	internally	internally	RB
10_1101-436634	67	5	relies	rely	VBZ
10_1101-436634	67	6	on	on	IN
10_1101-436634	67	7	variants	variant	NNS
10_1101-436634	67	8	annotate	annotate	JJ
10_1101-436634	67	9	,	,	,
10_1101-436634	67	10	junctions	junction	NNS
10_1101-436634	67	11	extract	extract	NN
10_1101-436634	67	12	,	,	,
10_1101-436634	67	13	and	and	CC
10_1101-436634	67	14	junctions	junction	NNS
10_1101-436634	67	15	annotate	annotate	JJ
10_1101-436634	67	16	to	to	TO
10_1101-436634	67	17	output	output	VB
10_1101-436634	67	18	a	a	DT
10_1101-436634	67	19	TSV	TSV	NNP
10_1101-436634	67	20	containing	contain	VBG
10_1101-436634	67	21	junctions	junction	NNS
10_1101-436634	67	22	proximal	proximal	JJ
10_1101-436634	67	23	to	to	IN
10_1101-436634	67	24	putatively	putatively	RB
10_1101-436634	67	25	splicing	splicing	VB
10_1101-436634	67	26	-	-	HYPH
10_1101-436634	67	27	relevant	relevant	JJ
10_1101-436634	67	28	variants	variant	NNS
10_1101-436634	67	29	.	.	.
10_1101-436634	68	1	The	the	DT
10_1101-436634	68	2	identify	identify	NN
10_1101-436634	68	3	pipeline	pipeline	NN
10_1101-436634	68	4	can	can	MD
10_1101-436634	68	5	be	be	VB
10_1101-436634	68	6	customized	customize	VBN
10_1101-436634	68	7	using	use	VBG
10_1101-436634	68	8	the	the	DT
10_1101-436634	68	9	same	same	JJ
10_1101-436634	68	10	parameters	parameter	NNS
10_1101-436634	68	11	as	as	IN
10_1101-436634	68	12	in	in	IN
10_1101-436634	68	13	the	the	DT
10_1101-436634	68	14	individual	individual	JJ
10_1101-436634	68	15	commands	command	NNS
10_1101-436634	68	16	.	.	.
10_1101-436634	69	1	Briefly	briefly	RB
10_1101-436634	69	2	,	,	,
10_1101-436634	69	3	cis	cis	NN
10_1101-436634	69	4	-	-	HYPH
10_1101-436634	69	5	splice	splice	NN
10_1101-436634	69	6	-	-	HYPH
10_1101-436634	69	7	effects	effect	NNS
10_1101-436634	69	8	identify	identify	VBP
10_1101-436634	69	9	first	first	JJ
10_1101-436634	69	10	performs	perform	VBZ
10_1101-436634	69	11	variants	variant	NNS
10_1101-436634	69	12	annotate	annotate	JJ
10_1101-436634	69	13	to	to	TO
10_1101-436634	69	14	determine	determine	VB
10_1101-436634	69	15	the	the	DT
10_1101-436634	69	16	splicing	splicing	NN
10_1101-436634	69	17	-	-	HYPH
10_1101-436634	69	18	relevance	relevance	NN
10_1101-436634	69	19	of	of	IN
10_1101-436634	69	20	each	each	DT
10_1101-436634	69	21	variant	variant	JJ
10_1101-436634	69	22	in	in	IN
10_1101-436634	69	23	the	the	DT
10_1101-436634	69	24	input	input	NN
10_1101-436634	69	25	VCF	vcf	NN
10_1101-436634	69	26	.	.	.
10_1101-436634	70	1	For	for	IN
10_1101-436634	70	2	each	each	DT
10_1101-436634	70	3	variant	variant	JJ
10_1101-436634	70	4	,	,	,
10_1101-436634	70	5	a	a	DT
10_1101-436634	70	6	“	"	``
10_1101-436634	70	7	splice	splice	NN
10_1101-436634	70	8	junction	junction	NN
10_1101-436634	70	9	region	region	NN
10_1101-436634	70	10	”	"	''
10_1101-436634	70	11	is	be	VBZ
10_1101-436634	70	12	determined	determine	VBN
10_1101-436634	70	13	by	by	IN
10_1101-436634	70	14	finding	find	VBG
10_1101-436634	70	15	the	the	DT
10_1101-436634	70	16	largest	large	JJS
10_1101-436634	70	17	span	span	NN
10_1101-436634	70	18	of	of	IN
10_1101-436634	70	19	sequence	sequence	NN
10_1101-436634	70	20	space	space	NN
10_1101-436634	70	21	between	between	IN
10_1101-436634	70	22	the	the	DT
10_1101-436634	70	23	exons	exon	NNS
10_1101-436634	70	24	that	that	WDT
10_1101-436634	70	25	flank	flank	VBP
10_1101-436634	70	26	the	the	DT
10_1101-436634	70	27	exon	exon	NNS
10_1101-436634	70	28	associated	associate	VBN
10_1101-436634	70	29	with	with	IN
10_1101-436634	70	30	the	the	DT
10_1101-436634	70	31	variant	variant	NN
10_1101-436634	70	32	.	.	.
10_1101-436634	71	1	From	from	IN
10_1101-436634	71	2	here	here	RB
10_1101-436634	71	3	,	,	,
10_1101-436634	71	4	junctions	junction	NNS
10_1101-436634	71	5	extract	extract	VBP
10_1101-436634	71	6	identifies	identifie	NNS
10_1101-436634	71	7	splicing	splice	VBG
10_1101-436634	71	8	junctions	junction	NNS
10_1101-436634	71	9	present	present	JJ
10_1101-436634	71	10	in	in	IN
10_1101-436634	71	11	the	the	DT
10_1101-436634	71	12	RNA	RNA	NNP
10_1101-436634	71	13	-	-	HYPH
10_1101-436634	71	14	seq	seq	NN
10_1101-436634	71	15	BAM	BAM	NNP
10_1101-436634	71	16	.	.	.
10_1101-436634	72	1	Next	next	RB
10_1101-436634	72	2	,	,	,
10_1101-436634	72	3	junctions	junction	NNS
10_1101-436634	72	4	annotate	annotate	VBP
10_1101-436634	72	5	labels	label	NNS
10_1101-436634	72	6	each	each	DT
10_1101-436634	72	7	extracted	extract	VBN
10_1101-436634	72	8	junction	junction	NN
10_1101-436634	72	9	with	with	IN
10_1101-436634	72	10	information	information	NN
10_1101-436634	72	11	from	from	IN
10_1101-436634	72	12	the	the	DT
10_1101-436634	72	13	reference	reference	NN
10_1101-436634	72	14	transcriptome	transcriptome	VBN
10_1101-436634	72	15	as	as	IN
10_1101-436634	72	16	described	describe	VBN
10_1101-436634	72	17	above	above	IN
10_1101-436634	72	18	and	and	CC
10_1101-436634	72	19	its	-PRON-	PRP$
10_1101-436634	72	20	associated	associate	VBN
10_1101-436634	72	21	variants	variant	NNS
10_1101-436634	72	22	based	base	VBN
10_1101-436634	72	23	on	on	IN
10_1101-436634	72	24	splice	splice	NN
10_1101-436634	72	25	junction	junction	NN
10_1101-436634	72	26	region	region	NN
10_1101-436634	72	27	overlap	overlap	NN
10_1101-436634	72	28	(	(	-LRB-
10_1101-436634	72	29	Figure	figure	NN
10_1101-436634	72	30	1C	1c	NN
10_1101-436634	72	31	)	)	-RRB-
10_1101-436634	72	32	.	.	.
10_1101-436634	73	1	For	for	IN
10_1101-436634	73	2	our	-PRON-	PRP$
10_1101-436634	73	3	analysis	analysis	NN
10_1101-436634	73	4	,	,	,
10_1101-436634	73	5	we	-PRON-	PRP
10_1101-436634	73	6	annotated	annotate	VBD
10_1101-436634	73	7	the	the	DT
10_1101-436634	73	8	pairs	pair	NNS
10_1101-436634	73	9	of	of	IN
10_1101-436634	73	10	associated	associated	JJ
10_1101-436634	73	11	variants	variant	NNS
10_1101-436634	73	12	and	and	CC
10_1101-436634	73	13	junctions	junction	NNS
10_1101-436634	73	14	identified	identify	VBN
10_1101-436634	73	15	by	by	IN
10_1101-436634	73	16	RegTools	RegTools	NNP
10_1101-436634	73	17	,	,	,
10_1101-436634	73	18	which	which	WDT
10_1101-436634	73	19	we	-PRON-	PRP
10_1101-436634	73	20	refer	refer	VBP
10_1101-436634	73	21	to	to	IN
10_1101-436634	73	22	as	as	IN
10_1101-436634	73	23	“	"	``
10_1101-436634	73	24	events	event	NNS
10_1101-436634	73	25	”	"	''
10_1101-436634	73	26	,	,	,
10_1101-436634	73	27	with	with	IN
10_1101-436634	73	28	additional	additional	JJ
10_1101-436634	73	29	information	information	NN
10_1101-436634	73	30	such	such	JJ
10_1101-436634	73	31	as	as	IN
10_1101-436634	73	32	whether	whether	IN
10_1101-436634	73	33	this	this	DT
10_1101-436634	73	34	association	association	NN
10_1101-436634	73	35	was	be	VBD
10_1101-436634	73	36	identified	identify	VBN
10_1101-436634	73	37	by	by	IN
10_1101-436634	73	38	a	a	DT
10_1101-436634	73	39	comparable	comparable	JJ
10_1101-436634	73	40	tool	tool	NN
10_1101-436634	73	41	,	,	,
10_1101-436634	73	42	the	the	DT
10_1101-436634	73	43	junction	junction	NN
10_1101-436634	73	44	was	be	VBD
10_1101-436634	73	45	found	find	VBN
10_1101-436634	73	46	in	in	IN
10_1101-436634	73	47	GTEx	GTEx	NNS
10_1101-436634	73	48	,	,	,
10_1101-436634	73	49	and	and	CC
10_1101-436634	73	50	whether	whether	IN
10_1101-436634	73	51	the	the	DT
10_1101-436634	73	52	event	event	NN
10_1101-436634	73	53	occurred	occur	VBD
10_1101-436634	73	54	in	in	IN
10_1101-436634	73	55	a	a	DT
10_1101-436634	73	56	cancer	cancer	NN
10_1101-436634	73	57	gene	gene	NN
10_1101-436634	73	58	according	accord	VBG
10_1101-436634	73	59	to	to	IN
10_1101-436634	73	60	Cancer	Cancer	NNP
10_1101-436634	73	61	Gene	Gene	NNP
10_1101-436634	73	62	Census	Census	NNP
10_1101-436634	73	63	(	(	-LRB-
10_1101-436634	73	64	CGC	CGC	NNP
10_1101-436634	73	65	)	)	-RRB-
10_1101-436634	73	66	(	(	-LRB-
10_1101-436634	73	67	Figure	Figure	NNP
10_1101-436634	73	68	1C)24,27	1C)24,27	NNP
10_1101-436634	73	69	.	.	.
10_1101-436634	74	1	Finally	finally	RB
10_1101-436634	74	2	,	,	,
10_1101-436634	74	3	we	-PRON-	PRP
10_1101-436634	74	4	created	create	VBD
10_1101-436634	74	5	IGV	IGV	NNP
10_1101-436634	74	6	sessions	session	NNS
10_1101-436634	74	7	for	for	IN
10_1101-436634	74	8	each	each	DT
10_1101-436634	74	9	event	event	NN
10_1101-436634	74	10	identified	identify	VBN
10_1101-436634	74	11	by	by	IN
10_1101-436634	74	12	RegTools	regtool	NNS
10_1101-436634	74	13	that	that	WDT
10_1101-436634	74	14	contained	contain	VBD
10_1101-436634	74	15	a	a	DT
10_1101-436634	74	16	bed	bed	NN
10_1101-436634	74	17	file	file	NN
10_1101-436634	74	18	with	with	IN
10_1101-436634	74	19	the	the	DT
10_1101-436634	74	20	junction	junction	NN
10_1101-436634	74	21	,	,	,
10_1101-436634	74	22	a	a	DT
10_1101-436634	74	23	VCF	VCF	NNP
10_1101-436634	74	24	file	file	NN
10_1101-436634	74	25	with	with	IN
10_1101-436634	74	26	the	the	DT
10_1101-436634	74	27	variant	variant	NN
10_1101-436634	74	28	,	,	,
10_1101-436634	74	29	and	and	CC
10_1101-436634	74	30	an	an	DT
10_1101-436634	74	31	alignment	alignment	NN
10_1101-436634	74	32	(	(	-LRB-
10_1101-436634	74	33	BAM	BAM	NNP
10_1101-436634	74	34	)	)	-RRB-
10_1101-436634	74	35	file	file	NN
10_1101-436634	74	36	for	for	IN
10_1101-436634	74	37	each	each	DT
10_1101-436634	74	38	sample	sample	NN
10_1101-436634	74	39	that	that	WDT
10_1101-436634	74	40	contained	contain	VBD
10_1101-436634	74	41	the	the	DT
10_1101-436634	74	42	variant28	variant28	NNP
10_1101-436634	74	43	.	.	.
10_1101-436634	75	1	These	these	DT
10_1101-436634	75	2	IGV	IGV	NNP
10_1101-436634	75	3	sessions	session	NNS
10_1101-436634	75	4	were	be	VBD
10_1101-436634	75	5	used	use	VBN
10_1101-436634	75	6	to	to	TO
10_1101-436634	75	7	manually	manually	RB
10_1101-436634	75	8	review	review	VB
10_1101-436634	75	9	candidate	candidate	NN
10_1101-436634	75	10	events	event	NNS
10_1101-436634	75	11	to	to	TO
10_1101-436634	75	12	assess	assess	VB
10_1101-436634	75	13	whether	whether	IN
10_1101-436634	75	14	the	the	DT
10_1101-436634	75	15	association	association	NN
10_1101-436634	75	16	between	between	IN
10_1101-436634	75	17	the	the	DT
10_1101-436634	75	18	variant	variant	JJ
10_1101-436634	75	19	and	and	CC
10_1101-436634	75	20	junction	junction	NN
10_1101-436634	75	21	makes	make	VBZ
10_1101-436634	75	22	sense	sense	NN
10_1101-436634	75	23	in	in	IN
10_1101-436634	75	24	a	a	DT
10_1101-436634	75	25	biological	biological	JJ
10_1101-436634	75	26	context	context	NN
10_1101-436634	75	27	.	.	.
10_1101-436634	76	1	RegTools	RegTools	NNP
10_1101-436634	76	2	is	be	VBZ
10_1101-436634	76	3	designed	design	VBN
10_1101-436634	76	4	for	for	IN
10_1101-436634	76	5	broad	broad	JJ
10_1101-436634	76	6	applicability	applicability	NN
10_1101-436634	76	7	and	and	CC
10_1101-436634	76	8	computational	computational	JJ
10_1101-436634	76	9	efficiency	efficiency	NN
10_1101-436634	76	10	.	.	.
10_1101-436634	77	1	By	by	IN
10_1101-436634	77	2	relying	rely	VBG
10_1101-436634	77	3	on	on	IN
10_1101-436634	77	4	well-	well-	JJ
10_1101-436634	77	5	established	establish	VBN
10_1101-436634	77	6	standards	standard	NNS
10_1101-436634	77	7	for	for	IN
10_1101-436634	77	8	sequence	sequence	NN
10_1101-436634	77	9	alignments	alignment	NNS
10_1101-436634	77	10	,	,	,
10_1101-436634	77	11	annotation	annotation	NN
10_1101-436634	77	12	files	file	NNS
10_1101-436634	77	13	,	,	,
10_1101-436634	77	14	and	and	CC
10_1101-436634	77	15	variant	variant	JJ
10_1101-436634	77	16	calls	call	NNS
10_1101-436634	77	17	and	and	CC
10_1101-436634	77	18	by	by	IN
10_1101-436634	77	19	remaining	remain	VBG
10_1101-436634	77	20	agnostic	agnostic	JJ
10_1101-436634	77	21	to	to	TO
10_1101-436634	77	22	downstream	downstream	JJ
10_1101-436634	77	23	statistical	statistical	JJ
10_1101-436634	77	24	methods	method	NNS
10_1101-436634	77	25	and	and	CC
10_1101-436634	77	26	comparisons	comparison	NNS
10_1101-436634	77	27	,	,	,
10_1101-436634	77	28	our	-PRON-	PRP$
10_1101-436634	77	29	tool	tool	NN
10_1101-436634	77	30	can	can	MD
10_1101-436634	77	31	be	be	VB
10_1101-436634	77	32	applied	apply	VBN
10_1101-436634	77	33	to	to	IN
10_1101-436634	77	34	a	a	DT
10_1101-436634	77	35	broad	broad	JJ
10_1101-436634	77	36	set	set	NN
10_1101-436634	77	37	of	of	IN
10_1101-436634	77	38	scientific	scientific	JJ
10_1101-436634	77	39	queries	query	NNS
10_1101-436634	77	40	and	and	CC
10_1101-436634	77	41	datasets	dataset	NNS
10_1101-436634	77	42	.	.	.
10_1101-436634	78	1	Moreover	moreover	RB
10_1101-436634	78	2	,	,	,
10_1101-436634	78	3	performance	performance	NN
10_1101-436634	78	4	tests	test	NNS
10_1101-436634	78	5	show	show	VBP
10_1101-436634	78	6	that	that	IN
10_1101-436634	78	7	cis-	cis-	IN
10_1101-436634	78	8	splice	splice	NN
10_1101-436634	78	9	-	-	HYPH
10_1101-436634	78	10	effects	effect	NNS
10_1101-436634	78	11	identify	identify	VBP
10_1101-436634	78	12	can	can	MD
10_1101-436634	78	13	process	process	VB
10_1101-436634	78	14	a	a	DT
10_1101-436634	78	15	typical	typical	JJ
10_1101-436634	78	16	candidate	candidate	NN
10_1101-436634	78	17	variant	variant	JJ
10_1101-436634	78	18	list	list	NN
10_1101-436634	78	19	of	of	IN
10_1101-436634	78	20	1,500,000	1,500,000	CD
10_1101-436634	78	21	variants	variant	NNS
10_1101-436634	78	22	and	and	CC
10_1101-436634	78	23	a	a	DT
10_1101-436634	78	24	corresponding	corresponding	JJ
10_1101-436634	78	25	RNA	RNA	NNP
10_1101-436634	78	26	-	-	HYPH
10_1101-436634	78	27	seq	seq	NN
10_1101-436634	78	28	BAM	BAM	NNP
10_1101-436634	78	29	file	file	NN
10_1101-436634	78	30	of	of	IN
10_1101-436634	78	31	82,807,868	82,807,868	CD
10_1101-436634	78	32	reads	read	NNS
10_1101-436634	78	33	in	in	IN
10_1101-436634	78	34	just	just	RB
10_1101-436634	78	35	~8	~8	NFP
10_1101-436634	78	36	minutes	minute	NNS
10_1101-436634	78	37	(	(	-LRB-
10_1101-436634	78	38	Supplementary	Supplementary	NNP
10_1101-436634	78	39	Figure	Figure	NNP
10_1101-436634	78	40	1	1	CD
10_1101-436634	78	41	)	)	-RRB-
10_1101-436634	78	42	.	.	.
10_1101-436634	79	1	Pan	pan	JJ
10_1101-436634	79	2	-	-	JJ
10_1101-436634	79	3	cancer	cancer	JJ
10_1101-436634	79	4	analysis	analysis	NN
10_1101-436634	79	5	of	of	IN
10_1101-436634	79	6	35	35	CD
10_1101-436634	79	7	tumor	tumor	NN
10_1101-436634	79	8	types	type	NNS
10_1101-436634	79	9	identifies	identify	VBZ
10_1101-436634	79	10	somatic	somatic	JJ
10_1101-436634	79	11	variants	variant	NNS
10_1101-436634	79	12	that	that	WDT
10_1101-436634	79	13	alter	alter	VBP
10_1101-436634	79	14	canonical	canonical	JJ
10_1101-436634	79	15	splicing	splicing	NN
10_1101-436634	79	16	RegTools	RegTools	NNP
10_1101-436634	79	17	was	be	VBD
10_1101-436634	79	18	applied	apply	VBN
10_1101-436634	79	19	to	to	IN
10_1101-436634	79	20	9,173	9,173	CD
10_1101-436634	79	21	samples	sample	NNS
10_1101-436634	79	22	over	over	IN
10_1101-436634	79	23	35	35	CD
10_1101-436634	79	24	cancer	cancer	NN
10_1101-436634	79	25	types	type	NNS
10_1101-436634	79	26	.	.	.
10_1101-436634	80	1	32	32	CD
10_1101-436634	80	2	of	of	IN
10_1101-436634	80	3	these	these	DT
10_1101-436634	80	4	cohorts	cohort	NNS
10_1101-436634	80	5	came	come	VBD
10_1101-436634	80	6	from	from	IN
10_1101-436634	80	7	TCGA	TCGA	NNP
10_1101-436634	80	8	while	while	IN
10_1101-436634	80	9	the	the	DT
10_1101-436634	80	10	remaining	remain	VBG
10_1101-436634	80	11	three	three	CD
10_1101-436634	80	12	were	be	VBD
10_1101-436634	80	13	obtained	obtain	VBN
10_1101-436634	80	14	from	from	IN
10_1101-436634	80	15	other	other	JJ
10_1101-436634	80	16	projects	project	NNS
10_1101-436634	80	17	being	be	VBG
10_1101-436634	80	18	conducted	conduct	VBN
10_1101-436634	80	19	at	at	IN
10_1101-436634	80	20	MGI	MGI	NNP
10_1101-436634	80	21	.	.	.
10_1101-436634	81	1	Cohort	cohort	NN
10_1101-436634	81	2	sizes	size	NNS
10_1101-436634	81	3	ranged	range	VBD
10_1101-436634	81	4	from	from	IN
10_1101-436634	81	5	21	21	CD
10_1101-436634	81	6	to	to	TO
10_1101-436634	81	7	1,022	1,022	CD
10_1101-436634	81	8	samples	sample	NNS
10_1101-436634	81	9	.	.	.
10_1101-436634	82	1	In	in	IN
10_1101-436634	82	2	total	total	JJ
10_1101-436634	82	3	,	,	,
10_1101-436634	82	4	6,370,631	6,370,631	CD
10_1101-436634	82	5	variants	variant	NNS
10_1101-436634	82	6	(	(	-LRB-
10_1101-436634	82	7	Figure	Figure	NNP
10_1101-436634	82	8	2A	2a	NN
10_1101-436634	82	9	)	)	-RRB-
10_1101-436634	82	10	and	and	CC
10_1101-436634	82	11	2,387,989,201	2,387,989,201	CD
10_1101-436634	82	12	junction	junction	NN
10_1101-436634	82	13	observations	observation	NNS
10_1101-436634	82	14	(	(	-LRB-
10_1101-436634	82	15	Figure	figure	NN
10_1101-436634	82	16	2B	2b	NN
10_1101-436634	82	17	)	)	-RRB-
10_1101-436634	82	18	were	be	VBD
10_1101-436634	82	19	analyzed	analyze	VBN
10_1101-436634	82	20	by	by	IN
10_1101-436634	82	21	RegTools	RegTools	NNP
10_1101-436634	82	22	.	.	.
10_1101-436634	83	1	By	by	IN
10_1101-436634	83	2	comparing	compare	VBG
10_1101-436634	83	3	the	the	DT
10_1101-436634	83	4	number	number	NN
10_1101-436634	83	5	of	of	IN
10_1101-436634	83	6	initial	initial	JJ
10_1101-436634	83	7	variants	variant	NNS
10_1101-436634	83	8	per	per	IN
10_1101-436634	83	9	cohort	cohort	NN
10_1101-436634	83	10	to	to	IN
10_1101-436634	83	11	the	the	DT
10_1101-436634	83	12	number	number	NN
10_1101-436634	83	13	of	of	IN
10_1101-436634	83	14	statistically	statistically	RB
10_1101-436634	83	15	significant	significant	JJ
10_1101-436634	83	16	variants	variant	NNS
10_1101-436634	83	17	,	,	,
10_1101-436634	83	18	we	-PRON-	PRP
10_1101-436634	83	19	.CC	.CC	:
10_1101-436634	83	20	-	-	:
10_1101-436634	83	21	BY	by	IN
10_1101-436634	83	22	-	-	HYPH
10_1101-436634	83	23	NC	NC	NNP
10_1101-436634	83	24	-	-	HYPH
10_1101-436634	83	25	ND	ND	NNP
10_1101-436634	83	26	4.0	4.0	CD
10_1101-436634	83	27	International	international	JJ
10_1101-436634	83	28	licensea	licensea	NNS
10_1101-436634	83	29	certified	certify	VBN
10_1101-436634	83	30	by	by	IN
10_1101-436634	83	31	peer	peer	NN
10_1101-436634	83	32	review	review	NN
10_1101-436634	83	33	)	)	-RRB-
10_1101-436634	83	34	is	be	VBZ
10_1101-436634	83	35	the	the	DT
10_1101-436634	83	36	author	author	NN
10_1101-436634	83	37	/	/	SYM
10_1101-436634	83	38	funder	funder	NN
10_1101-436634	83	39	,	,	,
10_1101-436634	83	40	who	who	WP
10_1101-436634	83	41	has	have	VBZ
10_1101-436634	83	42	granted	grant	VBN
10_1101-436634	83	43	bioRxiv	biorxiv	IN
10_1101-436634	83	44	a	a	DT
10_1101-436634	83	45	license	license	NN
10_1101-436634	83	46	to	to	TO
10_1101-436634	83	47	display	display	VB
10_1101-436634	83	48	the	the	DT
10_1101-436634	83	49	preprint	preprint	NN
10_1101-436634	83	50	in	in	IN
10_1101-436634	83	51	perpetuity	perpetuity	NN
10_1101-436634	83	52	.	.	.
10_1101-436634	84	1	It	-PRON-	PRP
10_1101-436634	84	2	is	be	VBZ
10_1101-436634	84	3	made	make	VBN
10_1101-436634	84	4	available	available	JJ
10_1101-436634	84	5	under	under	IN
10_1101-436634	84	6	The	the	DT
10_1101-436634	84	7	copyright	copyright	NN
10_1101-436634	84	8	holder	holder	NN
10_1101-436634	84	9	for	for	IN
10_1101-436634	84	10	this	this	DT
10_1101-436634	84	11	preprint	preprint	NN
10_1101-436634	84	12	(	(	-LRB-
10_1101-436634	84	13	which	which	WDT
10_1101-436634	84	14	was	be	VBD
10_1101-436634	84	15	notthis	notthis	DT
10_1101-436634	84	16	version	version	NN
10_1101-436634	84	17	posted	post	VBN
10_1101-436634	84	18	January	January	NNP
10_1101-436634	84	19	5	5	CD
10_1101-436634	84	20	,	,	,
10_1101-436634	84	21	2021	2021	CD
10_1101-436634	84	22	.	.	.
10_1101-436634	84	23	;	;	:
10_1101-436634	84	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	84	25	:	:	:
10_1101-436634	84	26	bioRxiv	biorxiv	VB
10_1101-436634	84	27	preprint	preprint	NN
10_1101-436634	84	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	84	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	84	30	5	5	CD
10_1101-436634	84	31	were	be	VBD
10_1101-436634	84	32	able	able	JJ
10_1101-436634	84	33	to	to	TO
10_1101-436634	84	34	show	show	VB
10_1101-436634	84	35	that	that	IN
10_1101-436634	84	36	RegTools	RegTools	NNP
10_1101-436634	84	37	produces	produce	VBZ
10_1101-436634	84	38	a	a	DT
10_1101-436634	84	39	prioritized	prioritize	VBN
10_1101-436634	84	40	list	list	NN
10_1101-436634	84	41	of	of	IN
10_1101-436634	84	42	potential	potential	JJ
10_1101-436634	84	43	splice	splice	NN
10_1101-436634	84	44	relevant	relevant	JJ
10_1101-436634	84	45	variants	variant	NNS
10_1101-436634	84	46	(	(	-LRB-
10_1101-436634	84	47	Supplementary	Supplementary	NNP
10_1101-436634	84	48	Figure	Figure	NNP
10_1101-436634	84	49	2	2	CD
10_1101-436634	84	50	)	)	-RRB-
10_1101-436634	84	51	.	.	.
10_1101-436634	85	1	Additionally	additionally	RB
10_1101-436634	85	2	,	,	,
10_1101-436634	85	3	when	when	WRB
10_1101-436634	85	4	analyzing	analyze	VBG
10_1101-436634	85	5	the	the	DT
10_1101-436634	85	6	junctions	junction	NNS
10_1101-436634	85	7	within	within	IN
10_1101-436634	85	8	each	each	DT
10_1101-436634	85	9	sample	sample	NN
10_1101-436634	85	10	,	,	,
10_1101-436634	85	11	we	-PRON-	PRP
10_1101-436634	85	12	found	find	VBD
10_1101-436634	85	13	that	that	IN
10_1101-436634	85	14	junctions	junction	NNS
10_1101-436634	85	15	present	present	JJ
10_1101-436634	85	16	in	in	IN
10_1101-436634	85	17	the	the	DT
10_1101-436634	85	18	reference	reference	NN
10_1101-436634	85	19	transcriptome	transcriptome	VBN
10_1101-436634	85	20	are	be	VBP
10_1101-436634	85	21	frequently	frequently	RB
10_1101-436634	85	22	seen	see	VBN
10_1101-436634	85	23	within	within	IN
10_1101-436634	85	24	GTEx	GTEx	NNP
10_1101-436634	85	25	data	datum	NNS
10_1101-436634	85	26	while	while	IN
10_1101-436634	85	27	junctions	junction	NNS
10_1101-436634	85	28	observed	observe	VBN
10_1101-436634	85	29	from	from	IN
10_1101-436634	85	30	a	a	DT
10_1101-436634	85	31	sample	sample	NN
10_1101-436634	85	32	’s	’s	POS
10_1101-436634	85	33	own	own	JJ
10_1101-436634	85	34	transcriptome	transcriptome	DT
10_1101-436634	85	35	data	datum	NNS
10_1101-436634	85	36	that	that	WDT
10_1101-436634	85	37	were	be	VBD
10_1101-436634	85	38	not	not	RB
10_1101-436634	85	39	present	present	JJ
10_1101-436634	85	40	in	in	IN
10_1101-436634	85	41	the	the	DT
10_1101-436634	85	42	reference	reference	NN
10_1101-436634	85	43	are	be	VBP
10_1101-436634	85	44	rarely	rarely	RB
10_1101-436634	85	45	seen	see	VBN
10_1101-436634	85	46	within	within	IN
10_1101-436634	85	47	GTEx	GTEx	NNS
10_1101-436634	85	48	(	(	-LRB-
10_1101-436634	85	49	Supplementary	Supplementary	NNP
10_1101-436634	85	50	Figure	Figure	NNP
10_1101-436634	85	51	3	3	CD
10_1101-436634	85	52	)	)	-RRB-
10_1101-436634	85	53	.	.	.
10_1101-436634	86	1	235,778	235,778	CD
10_1101-436634	86	2	significant	significant	JJ
10_1101-436634	86	3	variant	variant	JJ
10_1101-436634	86	4	junction	junction	NN
10_1101-436634	86	5	pairings	pairing	NNS
10_1101-436634	86	6	were	be	VBD
10_1101-436634	86	7	found	find	VBN
10_1101-436634	86	8	for	for	IN
10_1101-436634	86	9	junctions	junction	NNS
10_1101-436634	86	10	that	that	WDT
10_1101-436634	86	11	use	use	VBP
10_1101-436634	86	12	a	a	DT
10_1101-436634	86	13	known	know	VBN
10_1101-436634	86	14	donor	donor	NN
10_1101-436634	86	15	and	and	CC
10_1101-436634	86	16	novel	novel	JJ
10_1101-436634	86	17	acceptor	acceptor	NN
10_1101-436634	86	18	(	(	-LRB-
10_1101-436634	86	19	D	D	NNP
10_1101-436634	86	20	)	)	-RRB-
10_1101-436634	86	21	,	,	,
10_1101-436634	86	22	novel	novel	JJ
10_1101-436634	86	23	donor	donor	NN
10_1101-436634	86	24	and	and	CC
10_1101-436634	86	25	known	know	VBN
10_1101-436634	86	26	acceptor	acceptor	NN
10_1101-436634	86	27	(	(	-LRB-
10_1101-436634	86	28	A	a	NN
10_1101-436634	86	29	)	)	-RRB-
10_1101-436634	86	30	,	,	,
10_1101-436634	86	31	or	or	CC
10_1101-436634	86	32	novel	novel	JJ
10_1101-436634	86	33	combination	combination	NN
10_1101-436634	86	34	of	of	IN
10_1101-436634	86	35	a	a	DT
10_1101-436634	86	36	known	know	VBN
10_1101-436634	86	37	donor	donor	NN
10_1101-436634	86	38	and	and	CC
10_1101-436634	86	39	a	a	DT
10_1101-436634	86	40	known	know	VBN
10_1101-436634	86	41	acceptor	acceptor	NN
10_1101-436634	86	42	(	(	-LRB-
10_1101-436634	86	43	NDA	NDA	NNP
10_1101-436634	86	44	)	)	-RRB-
10_1101-436634	86	45	,	,	,
10_1101-436634	86	46	with	with	IN
10_1101-436634	86	47	novel	novel	NN
10_1101-436634	86	48	here	here	RB
10_1101-436634	86	49	meaning	mean	VBG
10_1101-436634	86	50	that	that	IN
10_1101-436634	86	51	the	the	DT
10_1101-436634	86	52	junction	junction	NN
10_1101-436634	86	53	was	be	VBD
10_1101-436634	86	54	not	not	RB
10_1101-436634	86	55	found	find	VBN
10_1101-436634	86	56	in	in	IN
10_1101-436634	86	57	the	the	DT
10_1101-436634	86	58	reference	reference	NN
10_1101-436634	86	59	transcriptome	transcriptome	VBN
10_1101-436634	86	60	(	(	-LRB-
10_1101-436634	86	61	Methods	method	NNS
10_1101-436634	86	62	,	,	,
10_1101-436634	86	63	Figure	figure	NN
10_1101-436634	86	64	2C	2c	NN
10_1101-436634	86	65	,	,	,
10_1101-436634	86	66	Supplemental	Supplemental	NNP
10_1101-436634	86	67	Files	Files	NNP
10_1101-436634	86	68	1	1	CD
10_1101-436634	86	69	and	and	CC
10_1101-436634	86	70	2	2	CD
10_1101-436634	86	71	)	)	-RRB-
10_1101-436634	86	72	.	.	.
10_1101-436634	87	1	While	while	IN
10_1101-436634	87	2	our	-PRON-	PRP$
10_1101-436634	87	3	analysis	analysis	NN
10_1101-436634	87	4	primarily	primarily	RB
10_1101-436634	87	5	focuses	focus	VBZ
10_1101-436634	87	6	on	on	IN
10_1101-436634	87	7	variants	variant	NNS
10_1101-436634	87	8	in	in	IN
10_1101-436634	87	9	relation	relation	NN
10_1101-436634	87	10	to	to	IN
10_1101-436634	87	11	novel	novel	JJ
10_1101-436634	87	12	splice	splice	NN
10_1101-436634	87	13	events	event	NNS
10_1101-436634	87	14	because	because	IN
10_1101-436634	87	15	of	of	IN
10_1101-436634	87	16	the	the	DT
10_1101-436634	87	17	potential	potential	JJ
10_1101-436634	87	18	importance	importance	NN
10_1101-436634	87	19	of	of	IN
10_1101-436634	87	20	these	these	DT
10_1101-436634	87	21	events	event	NNS
10_1101-436634	87	22	within	within	IN
10_1101-436634	87	23	tumor	tumor	NN
10_1101-436634	87	24	processes	process	NNS
10_1101-436634	87	25	,	,	,
10_1101-436634	87	26	we	-PRON-	PRP
10_1101-436634	87	27	also	also	RB
10_1101-436634	87	28	wanted	want	VBD
10_1101-436634	87	29	to	to	TO
10_1101-436634	87	30	assess	assess	VB
10_1101-436634	87	31	how	how	WRB
10_1101-436634	87	32	often	often	RB
10_1101-436634	87	33	a	a	DT
10_1101-436634	87	34	variant	variant	NN
10_1101-436634	87	35	was	be	VBD
10_1101-436634	87	36	significantly	significantly	RB
10_1101-436634	87	37	associated	associate	VBN
10_1101-436634	87	38	with	with	IN
10_1101-436634	87	39	a	a	DT
10_1101-436634	87	40	known	know	VBN
10_1101-436634	87	41	junction	junction	NN
10_1101-436634	87	42	.	.	.
10_1101-436634	88	1	5,157	5,157	CD
10_1101-436634	88	2	variant	variant	JJ
10_1101-436634	88	3	junction	junction	NN
10_1101-436634	88	4	pairings	pairing	NNS
10_1101-436634	88	5	were	be	VBD
10_1101-436634	88	6	found	find	VBN
10_1101-436634	88	7	for	for	IN
10_1101-436634	88	8	junctions	junction	NNS
10_1101-436634	88	9	known	know	VBN
10_1101-436634	88	10	to	to	IN
10_1101-436634	88	11	the	the	DT
10_1101-436634	88	12	reference	reference	NN
10_1101-436634	88	13	(	(	-LRB-
10_1101-436634	88	14	DA	DA	NNP
10_1101-436634	88	15	junctions	junction	NNS
10_1101-436634	88	16	)	)	-RRB-
10_1101-436634	88	17	(	(	-LRB-
10_1101-436634	88	18	Supplemental	Supplemental	NNP
10_1101-436634	88	19	Files	Files	NNP
10_1101-436634	88	20	3	3	CD
10_1101-436634	88	21	and	and	CC
10_1101-436634	88	22	4	4	CD
10_1101-436634	88	23	)	)	-RRB-
10_1101-436634	88	24	.	.	.
10_1101-436634	89	1	This	this	DT
10_1101-436634	89	2	finding	finding	NN
10_1101-436634	89	3	indicates	indicate	VBZ
10_1101-436634	89	4	that	that	IN
10_1101-436634	89	5	while	while	IN
10_1101-436634	89	6	splice	splice	NN
10_1101-436634	89	7	variants	variant	NNS
10_1101-436634	89	8	usually	usually	RB
10_1101-436634	89	9	result	result	VBP
10_1101-436634	89	10	in	in	IN
10_1101-436634	89	11	a	a	DT
10_1101-436634	89	12	novel	novel	JJ
10_1101-436634	89	13	junction	junction	NN
10_1101-436634	89	14	occurring	occur	VBG
10_1101-436634	89	15	,	,	,
10_1101-436634	89	16	they	-PRON-	PRP
10_1101-436634	89	17	sometimes	sometimes	RB
10_1101-436634	89	18	alter	alter	VBP
10_1101-436634	89	19	the	the	DT
10_1101-436634	89	20	expression	expression	NN
10_1101-436634	89	21	of	of	IN
10_1101-436634	89	22	known	know	VBN
10_1101-436634	89	23	junctions	junction	NNS
10_1101-436634	89	24	.	.	.
10_1101-436634	90	1	Generally	generally	RB
10_1101-436634	90	2	,	,	,
10_1101-436634	90	3	significant	significant	JJ
10_1101-436634	90	4	events	event	NNS
10_1101-436634	90	5	were	be	VBD
10_1101-436634	90	6	evenly	evenly	RB
10_1101-436634	90	7	split	split	VBN
10_1101-436634	90	8	among	among	IN
10_1101-436634	90	9	each	each	DT
10_1101-436634	90	10	of	of	IN
10_1101-436634	90	11	the	the	DT
10_1101-436634	90	12	novel	novel	JJ
10_1101-436634	90	13	junction	junction	NN
10_1101-436634	90	14	types	type	NNS
10_1101-436634	90	15	considered	consider	VBN
10_1101-436634	90	16	(	(	-LRB-
10_1101-436634	90	17	D	d	NN
10_1101-436634	90	18	,	,	,
10_1101-436634	90	19	A	a	NN
10_1101-436634	90	20	,	,	,
10_1101-436634	90	21	and	and	CC
10_1101-436634	90	22	NDA	NDA	NNP
10_1101-436634	90	23	)	)	-RRB-
10_1101-436634	90	24	.	.	.
10_1101-436634	91	1	The	the	DT
10_1101-436634	91	2	number	number	NN
10_1101-436634	91	3	of	of	IN
10_1101-436634	91	4	significant	significant	JJ
10_1101-436634	91	5	events	event	NNS
10_1101-436634	91	6	increased	increase	VBD
10_1101-436634	91	7	as	as	IN
10_1101-436634	91	8	the	the	DT
10_1101-436634	91	9	splice	splice	NN
10_1101-436634	91	10	variant	variant	JJ
10_1101-436634	91	11	window	window	NN
10_1101-436634	91	12	size	size	NN
10_1101-436634	91	13	increased	increase	VBD
10_1101-436634	91	14	,	,	,
10_1101-436634	91	15	with	with	IN
10_1101-436634	91	16	both	both	CC
10_1101-436634	91	17	the	the	DT
10_1101-436634	91	18	E	e	NN
10_1101-436634	91	19	and	and	CC
10_1101-436634	91	20	I	-PRON-	PRP
10_1101-436634	91	21	results	result	VBZ
10_1101-436634	91	22	being	be	VBG
10_1101-436634	91	23	comparable	comparable	JJ
10_1101-436634	91	24	in	in	IN
10_1101-436634	91	25	number	number	NN
10_1101-436634	91	26	.	.	.
10_1101-436634	92	1	Notably	notably	RB
10_1101-436634	92	2	,	,	,
10_1101-436634	92	3	hepatocellular	hepatocellular	JJ
10_1101-436634	92	4	carcinoma	carcinoma	NN
10_1101-436634	92	5	(	(	-LRB-
10_1101-436634	92	6	HCC	HCC	NNP
10_1101-436634	92	7	)	)	-RRB-
10_1101-436634	92	8	was	be	VBD
10_1101-436634	92	9	the	the	DT
10_1101-436634	92	10	only	only	JJ
10_1101-436634	92	11	cohort	cohort	NN
10_1101-436634	92	12	that	that	WDT
10_1101-436634	92	13	had	have	VBD
10_1101-436634	92	14	whole	whole	JJ
10_1101-436634	92	15	genome	genome	JJ
10_1101-436634	92	16	sequencing	sequencing	NN
10_1101-436634	92	17	(	(	-LRB-
10_1101-436634	92	18	WGS	WGS	NNP
10_1101-436634	92	19	)	)	-RRB-
10_1101-436634	92	20	data	datum	NNS
10_1101-436634	92	21	available	available	JJ
10_1101-436634	92	22	and	and	CC
10_1101-436634	92	23	,	,	,
10_1101-436634	92	24	as	as	IN
10_1101-436634	92	25	expected	expect	VBN
10_1101-436634	92	26	,	,	,
10_1101-436634	92	27	it	-PRON-	PRP
10_1101-436634	92	28	exhibited	exhibit	VBD
10_1101-436634	92	29	a	a	DT
10_1101-436634	92	30	marked	marked	JJ
10_1101-436634	92	31	increase	increase	NN
10_1101-436634	92	32	in	in	IN
10_1101-436634	92	33	the	the	DT
10_1101-436634	92	34	number	number	NN
10_1101-436634	92	35	of	of	IN
10_1101-436634	92	36	significant	significant	JJ
10_1101-436634	92	37	events	event	NNS
10_1101-436634	92	38	for	for	IN
10_1101-436634	92	39	its	-PRON-	PRP$
10_1101-436634	92	40	results	result	NNS
10_1101-436634	92	41	within	within	IN
10_1101-436634	92	42	the	the	DT
10_1101-436634	92	43	“	"	``
10_1101-436634	92	44	I	-PRON-	PRP
10_1101-436634	92	45	”	"	''
10_1101-436634	92	46	splice	splice	NN
10_1101-436634	92	47	variant	variant	JJ
10_1101-436634	92	48	window	window	NN
10_1101-436634	92	49	.	.	.
10_1101-436634	93	1	This	this	DT
10_1101-436634	93	2	observation	observation	NN
10_1101-436634	93	3	highlights	highlight	VBZ
10_1101-436634	93	4	the	the	DT
10_1101-436634	93	5	low	low	JJ
10_1101-436634	93	6	sequence	sequence	NN
10_1101-436634	93	7	coverage	coverage	NN
10_1101-436634	93	8	of	of	IN
10_1101-436634	93	9	intronic	intronic	JJ
10_1101-436634	93	10	regions	region	NNS
10_1101-436634	93	11	that	that	WDT
10_1101-436634	93	12	occurs	occur	VBZ
10_1101-436634	93	13	with	with	IN
10_1101-436634	93	14	WES	WES	NNP
10_1101-436634	93	15	which	which	WDT
10_1101-436634	93	16	subsequently	subsequently	RB
10_1101-436634	93	17	leads	lead	VBZ
10_1101-436634	93	18	to	to	IN
10_1101-436634	93	19	underpowered	underpowered	JJ
10_1101-436634	93	20	discovery	discovery	NN
10_1101-436634	93	21	of	of	IN
10_1101-436634	93	22	potential	potential	JJ
10_1101-436634	93	23	splice	splice	NN
10_1101-436634	93	24	altering	alter	VBG
10_1101-436634	93	25	variants	variant	NNS
10_1101-436634	93	26	within	within	IN
10_1101-436634	93	27	introns	intron	NNS
10_1101-436634	93	28	.	.	.
10_1101-436634	94	1	Variants	variant	NNS
10_1101-436634	94	2	were	be	VBD
10_1101-436634	94	3	analyzed	analyze	VBN
10_1101-436634	94	4	across	across	IN
10_1101-436634	94	5	tumor	tumor	NN
10_1101-436634	94	6	types	type	NNS
10_1101-436634	94	7	for	for	IN
10_1101-436634	94	8	how	how	WRB
10_1101-436634	94	9	often	often	RB
10_1101-436634	94	10	they	-PRON-	PRP
10_1101-436634	94	11	result	result	VBP
10_1101-436634	94	12	in	in	IN
10_1101-436634	94	13	either	either	CC
10_1101-436634	94	14	a	a	DT
10_1101-436634	94	15	single	single	JJ
10_1101-436634	94	16	or	or	CC
10_1101-436634	94	17	multiple	multiple	JJ
10_1101-436634	94	18	novel	novel	JJ
10_1101-436634	94	19	junctions	junction	NNS
10_1101-436634	94	20	(	(	-LRB-
10_1101-436634	94	21	Figure	Figure	NNP
10_1101-436634	94	22	3A	3A	NNP
10_1101-436634	94	23	)	)	-RRB-
10_1101-436634	94	24	.	.	.
10_1101-436634	95	1	While	while	IN
10_1101-436634	95	2	a	a	DT
10_1101-436634	95	3	single	single	JJ
10_1101-436634	95	4	variant	variant	NN
10_1101-436634	95	5	resulting	resulting	NN
10_1101-436634	95	6	in	in	IN
10_1101-436634	95	7	a	a	DT
10_1101-436634	95	8	single	single	JJ
10_1101-436634	95	9	novel	novel	NN
10_1101-436634	95	10	junction	junction	NN
10_1101-436634	95	11	is	be	VBZ
10_1101-436634	95	12	most	most	RBS
10_1101-436634	95	13	commonly	commonly	RB
10_1101-436634	95	14	observed	observe	VBN
10_1101-436634	95	15	(	(	-LRB-
10_1101-436634	95	16	72.27	72.27	CD
10_1101-436634	95	17	-	-	HYPH
10_1101-436634	95	18	83.78	83.78	CD
10_1101-436634	95	19	%	%	NN
10_1101-436634	95	20	)	)	-RRB-
10_1101-436634	95	21	,	,	,
10_1101-436634	95	22	a	a	DT
10_1101-436634	95	23	single	single	JJ
10_1101-436634	95	24	variant	variant	NN
10_1101-436634	95	25	also	also	RB
10_1101-436634	95	26	commonly	commonly	RB
10_1101-436634	95	27	results	result	VBZ
10_1101-436634	95	28	in	in	IN
10_1101-436634	95	29	multiple	multiple	JJ
10_1101-436634	95	30	junctions	junction	NNS
10_1101-436634	95	31	being	be	VBG
10_1101-436634	95	32	created	create	VBN
10_1101-436634	95	33	,	,	,
10_1101-436634	95	34	either	either	DT
10_1101-436634	95	35	of	of	IN
10_1101-436634	95	36	the	the	DT
10_1101-436634	95	37	same	same	JJ
10_1101-436634	95	38	type	type	NN
10_1101-436634	95	39	(	(	-LRB-
10_1101-436634	95	40	6.56	6.56	CD
10_1101-436634	95	41	-	-	SYM
10_1101-436634	95	42	10.94	10.94	CD
10_1101-436634	95	43	%	%	NN
10_1101-436634	95	44	)	)	-RRB-
10_1101-436634	95	45	or	or	CC
10_1101-436634	95	46	of	of	IN
10_1101-436634	95	47	different	different	JJ
10_1101-436634	95	48	types	type	NNS
10_1101-436634	95	49	(	(	-LRB-
10_1101-436634	95	50	9.66-	9.66-	CD
10_1101-436634	95	51	16.79	16.79	CD
10_1101-436634	95	52	%	%	NN
10_1101-436634	95	53	)	)	-RRB-
10_1101-436634	95	54	(	(	-LRB-
10_1101-436634	95	55	Figure	figure	NN
10_1101-436634	95	56	3B	3b	NN
10_1101-436634	95	57	)	)	-RRB-
10_1101-436634	95	58	.	.	.
10_1101-436634	96	1	Variants	variant	NNS
10_1101-436634	96	2	that	that	WDT
10_1101-436634	96	3	are	be	VBP
10_1101-436634	96	4	associated	associate	VBN
10_1101-436634	96	5	with	with	IN
10_1101-436634	96	6	multiple	multiple	JJ
10_1101-436634	96	7	novel	novel	JJ
10_1101-436634	96	8	junctions	junction	NNS
10_1101-436634	96	9	of	of	IN
10_1101-436634	96	10	different	different	JJ
10_1101-436634	96	11	types	type	NNS
10_1101-436634	96	12	were	be	VBD
10_1101-436634	96	13	further	further	RB
10_1101-436634	96	14	investigated	investigate	VBN
10_1101-436634	96	15	to	to	TO
10_1101-436634	96	16	identify	identify	VB
10_1101-436634	96	17	how	how	WRB
10_1101-436634	96	18	often	often	RB
10_1101-436634	96	19	a	a	DT
10_1101-436634	96	20	particular	particular	JJ
10_1101-436634	96	21	junction	junction	NN
10_1101-436634	96	22	type	type	NN
10_1101-436634	96	23	occurred	occur	VBD
10_1101-436634	96	24	with	with	IN
10_1101-436634	96	25	another	another	DT
10_1101-436634	96	26	(	(	-LRB-
10_1101-436634	96	27	Figure	figure	NN
10_1101-436634	96	28	3C	3c	NN
10_1101-436634	96	29	)	)	-RRB-
10_1101-436634	96	30	.	.	.
10_1101-436634	97	1	Most	most	RBS
10_1101-436634	97	2	commonly	commonly	RB
10_1101-436634	97	3	,	,	,
10_1101-436634	97	4	we	-PRON-	PRP
10_1101-436634	97	5	observed	observe	VBD
10_1101-436634	97	6	an	an	DT
10_1101-436634	97	7	alternate	alternate	JJ
10_1101-436634	97	8	donor	donor	NN
10_1101-436634	97	9	or	or	CC
10_1101-436634	97	10	acceptor	acceptor	NN
10_1101-436634	97	11	site	site	NN
10_1101-436634	97	12	being	be	VBG
10_1101-436634	97	13	used	use	VBN
10_1101-436634	97	14	in	in	IN
10_1101-436634	97	15	conjunction	conjunction	NN
10_1101-436634	97	16	with	with	IN
10_1101-436634	97	17	an	an	DT
10_1101-436634	97	18	exon	exon	JJ
10_1101-436634	97	19	skipping	skipping	NN
10_1101-436634	97	20	event	event	NN
10_1101-436634	97	21	.	.	.
10_1101-436634	98	1	These	these	DT
10_1101-436634	98	2	events	event	NNS
10_1101-436634	98	3	were	be	VBD
10_1101-436634	98	4	particularly	particularly	RB
10_1101-436634	98	5	common	common	JJ
10_1101-436634	98	6	within	within	IN
10_1101-436634	98	7	the	the	DT
10_1101-436634	98	8	default	default	NN
10_1101-436634	98	9	window	window	NN
10_1101-436634	98	10	(	(	-LRB-
10_1101-436634	98	11	2	2	CD
10_1101-436634	98	12	intronic	intronic	JJ
10_1101-436634	98	13	bases	basis	NNS
10_1101-436634	98	14	or	or	CC
10_1101-436634	98	15	3	3	CD
10_1101-436634	98	16	exonic	exonic	JJ
10_1101-436634	98	17	bases	basis	NNS
10_1101-436634	98	18	from	from	IN
10_1101-436634	98	19	the	the	DT
10_1101-436634	98	20	exon	exon	JJ
10_1101-436634	98	21	edge	edge	NN
10_1101-436634	98	22	)	)	-RRB-
10_1101-436634	98	23	,	,	,
10_1101-436634	98	24	as	as	IN
10_1101-436634	98	25	a	a	DT
10_1101-436634	98	26	SNV	SNV	NNP
10_1101-436634	98	27	or	or	CC
10_1101-436634	98	28	indel	indel	NN
10_1101-436634	98	29	within	within	IN
10_1101-436634	98	30	these	these	DT
10_1101-436634	98	31	positions	position	NNS
10_1101-436634	98	32	has	have	VBZ
10_1101-436634	98	33	a	a	DT
10_1101-436634	98	34	high	high	JJ
10_1101-436634	98	35	probability	probability	NN
10_1101-436634	98	36	of	of	IN
10_1101-436634	98	37	disrupting	disrupt	VBG
10_1101-436634	98	38	the	the	DT
10_1101-436634	98	39	natural	natural	JJ
10_1101-436634	98	40	splice	splice	NN
10_1101-436634	98	41	site	site	NN
10_1101-436634	98	42	,	,	,
10_1101-436634	98	43	thus	thus	RB
10_1101-436634	98	44	causing	cause	VBG
10_1101-436634	98	45	the	the	DT
10_1101-436634	98	46	splicing	splice	VBG
10_1101-436634	98	47	machinery	machinery	NN
10_1101-436634	98	48	to	to	TO
10_1101-436634	98	49	use	use	VB
10_1101-436634	98	50	a	a	DT
10_1101-436634	98	51	cryptic	cryptic	JJ
10_1101-436634	98	52	splice	splice	NN
10_1101-436634	98	53	site	site	NN
10_1101-436634	98	54	nearby	nearby	RB
10_1101-436634	98	55	or	or	CC
10_1101-436634	98	56	skip	skip	VBZ
10_1101-436634	98	57	the	the	DT
10_1101-436634	98	58	splice	splice	NN
10_1101-436634	98	59	site	site	NN
10_1101-436634	98	60	entirely	entirely	RB
10_1101-436634	98	61	.	.	.
10_1101-436634	99	1	The	the	DT
10_1101-436634	99	2	next	next	JJ
10_1101-436634	99	3	most	most	RBS
10_1101-436634	99	4	common	common	JJ
10_1101-436634	99	5	event	event	NN
10_1101-436634	99	6	was	be	VBD
10_1101-436634	99	7	an	an	DT
10_1101-436634	99	8	alternate	alternate	JJ
10_1101-436634	99	9	donor	donor	NN
10_1101-436634	99	10	site	site	NN
10_1101-436634	99	11	and	and	CC
10_1101-436634	99	12	an	an	DT
10_1101-436634	99	13	alternate	alternate	JJ
10_1101-436634	99	14	acceptor	acceptor	NN
10_1101-436634	99	15	site	site	NN
10_1101-436634	99	16	both	both	DT
10_1101-436634	99	17	being	be	VBG
10_1101-436634	99	18	used	use	VBN
10_1101-436634	99	19	as	as	IN
10_1101-436634	99	20	the	the	DT
10_1101-436634	99	21	result	result	NN
10_1101-436634	99	22	of	of	IN
10_1101-436634	99	23	a	a	DT
10_1101-436634	99	24	single	single	JJ
10_1101-436634	99	25	variant	variant	NN
10_1101-436634	99	26	.	.	.
10_1101-436634	100	1	The	the	DT
10_1101-436634	100	2	combination	combination	NN
10_1101-436634	100	3	of	of	IN
10_1101-436634	100	4	a	a	DT
10_1101-436634	100	5	novel	novel	JJ
10_1101-436634	100	6	acceptor	acceptor	NN
10_1101-436634	100	7	site	site	NN
10_1101-436634	100	8	and	and	CC
10_1101-436634	100	9	novel	novel	JJ
10_1101-436634	100	10	donor	donor	NN
10_1101-436634	100	11	site	site	NN
10_1101-436634	100	12	being	be	VBG
10_1101-436634	100	13	used	use	VBN
10_1101-436634	100	14	in	in	IN
10_1101-436634	100	15	conjunction	conjunction	NN
10_1101-436634	100	16	with	with	IN
10_1101-436634	100	17	an	an	DT
10_1101-436634	100	18	exon	exon	NN
10_1101-436634	100	19	-	-	HYPH
10_1101-436634	100	20	skipping	skip	VBG
10_1101-436634	100	21	event	event	NN
10_1101-436634	100	22	occurred	occur	VBD
10_1101-436634	100	23	the	the	DT
10_1101-436634	100	24	least	least	JJS
10_1101-436634	100	25	and	and	CC
10_1101-436634	100	26	occurrence	occurrence	NN
10_1101-436634	100	27	of	of	IN
10_1101-436634	100	28	this	this	DT
10_1101-436634	100	29	type	type	NN
10_1101-436634	100	30	of	of	IN
10_1101-436634	100	31	event	event	NN
10_1101-436634	100	32	remains	remain	VBZ
10_1101-436634	100	33	fairly	fairly	RB
10_1101-436634	100	34	low	low	JJ
10_1101-436634	100	35	,	,	,
10_1101-436634	100	36	even	even	RB
10_1101-436634	100	37	as	as	IN
10_1101-436634	100	38	the	the	DT
10_1101-436634	100	39	search	search	NN
10_1101-436634	100	40	space	space	NN
10_1101-436634	100	41	increases	increase	VBZ
10_1101-436634	100	42	within	within	IN
10_1101-436634	100	43	the	the	DT
10_1101-436634	100	44	larger	large	JJR
10_1101-436634	100	45	splice	splice	NN
10_1101-436634	100	46	variant	variant	JJ
10_1101-436634	100	47	windows	window	NNS
10_1101-436634	100	48	.	.	.
10_1101-436634	101	1	This	this	DT
10_1101-436634	101	2	finding	finding	NN
10_1101-436634	101	3	indicates	indicate	VBZ
10_1101-436634	101	4	the	the	DT
10_1101-436634	101	5	low	low	JJ
10_1101-436634	101	6	likelihood	likelihood	NN
10_1101-436634	101	7	of	of	IN
10_1101-436634	101	8	a	a	DT
10_1101-436634	101	9	single	single	JJ
10_1101-436634	101	10	variant	variant	NN
10_1101-436634	101	11	resulting	resulting	NN
10_1101-436634	101	12	in	in	IN
10_1101-436634	101	13	simultaneous	simultaneous	JJ
10_1101-436634	101	14	disruption	disruption	NN
10_1101-436634	101	15	of	of	IN
10_1101-436634	101	16	a	a	DT
10_1101-436634	101	17	splice	splice	NN
10_1101-436634	101	18	acceptor	acceptor	NN
10_1101-436634	101	19	and	and	CC
10_1101-436634	101	20	donor	donor	NN
10_1101-436634	101	21	as	as	RB
10_1101-436634	101	22	well	well	RB
10_1101-436634	101	23	as	as	IN
10_1101-436634	101	24	complete	complete	JJ
10_1101-436634	101	25	skipping	skipping	NN
10_1101-436634	101	26	of	of	IN
10_1101-436634	101	27	an	an	DT
10_1101-436634	101	28	exon	exon	NN
10_1101-436634	101	29	.	.	.
10_1101-436634	102	1	Overall	overall	RB
10_1101-436634	102	2	,	,	,
10_1101-436634	102	3	this	this	DT
10_1101-436634	102	4	analysis	analysis	NN
10_1101-436634	102	5	highlights	highlight	VBZ
10_1101-436634	102	6	that	that	IN
10_1101-436634	102	7	there	there	EX
10_1101-436634	102	8	is	be	VBZ
10_1101-436634	102	9	evidence	evidence	NN
10_1101-436634	102	10	that	that	IN
10_1101-436634	102	11	a	a	DT
10_1101-436634	102	12	single	single	JJ
10_1101-436634	102	13	variant	variant	NN
10_1101-436634	102	14	can	can	MD
10_1101-436634	102	15	lead	lead	VB
10_1101-436634	102	16	to	to	IN
10_1101-436634	102	17	multiple	multiple	JJ
10_1101-436634	102	18	novel	novel	JJ
10_1101-436634	102	19	junctions	junction	NNS
10_1101-436634	102	20	being	be	VBG
10_1101-436634	102	21	expressed	express	VBN
10_1101-436634	102	22	.	.	.
10_1101-436634	103	1	Tools	tool	NNS
10_1101-436634	103	2	that	that	WDT
10_1101-436634	103	3	only	only	RB
10_1101-436634	103	4	allow	allow	VBP
10_1101-436634	103	5	for	for	IN
10_1101-436634	103	6	a	a	DT
10_1101-436634	103	7	single	single	JJ
10_1101-436634	103	8	junction	junction	NN
10_1101-436634	103	9	to	to	TO
10_1101-436634	103	10	be	be	VB
10_1101-436634	103	11	predicted	predict	VBN
10_1101-436634	103	12	or	or	CC
10_1101-436634	103	13	.CC	.CC	:
10_1101-436634	103	14	-	-	HYPH
10_1101-436634	103	15	BY	by	IN
10_1101-436634	103	16	-	-	HYPH
10_1101-436634	103	17	NC	NC	NNP
10_1101-436634	103	18	-	-	HYPH
10_1101-436634	103	19	ND	ND	NNP
10_1101-436634	103	20	4.0	4.0	CD
10_1101-436634	103	21	International	international	JJ
10_1101-436634	103	22	licensea	licensea	NNS
10_1101-436634	103	23	certified	certify	VBN
10_1101-436634	103	24	by	by	IN
10_1101-436634	103	25	peer	peer	NN
10_1101-436634	103	26	review	review	NN
10_1101-436634	103	27	)	)	-RRB-
10_1101-436634	103	28	is	be	VBZ
10_1101-436634	103	29	the	the	DT
10_1101-436634	103	30	author	author	NN
10_1101-436634	103	31	/	/	SYM
10_1101-436634	103	32	funder	funder	NN
10_1101-436634	103	33	,	,	,
10_1101-436634	103	34	who	who	WP
10_1101-436634	103	35	has	have	VBZ
10_1101-436634	103	36	granted	grant	VBN
10_1101-436634	103	37	bioRxiv	biorxiv	IN
10_1101-436634	103	38	a	a	DT
10_1101-436634	103	39	license	license	NN
10_1101-436634	103	40	to	to	TO
10_1101-436634	103	41	display	display	VB
10_1101-436634	103	42	the	the	DT
10_1101-436634	103	43	preprint	preprint	NN
10_1101-436634	103	44	in	in	IN
10_1101-436634	103	45	perpetuity	perpetuity	NN
10_1101-436634	103	46	.	.	.
10_1101-436634	104	1	It	-PRON-	PRP
10_1101-436634	104	2	is	be	VBZ
10_1101-436634	104	3	made	make	VBN
10_1101-436634	104	4	available	available	JJ
10_1101-436634	104	5	under	under	IN
10_1101-436634	104	6	The	the	DT
10_1101-436634	104	7	copyright	copyright	NN
10_1101-436634	104	8	holder	holder	NN
10_1101-436634	104	9	for	for	IN
10_1101-436634	104	10	this	this	DT
10_1101-436634	104	11	preprint	preprint	NN
10_1101-436634	104	12	(	(	-LRB-
10_1101-436634	104	13	which	which	WDT
10_1101-436634	104	14	was	be	VBD
10_1101-436634	104	15	notthis	notthis	DT
10_1101-436634	104	16	version	version	NN
10_1101-436634	104	17	posted	post	VBN
10_1101-436634	104	18	January	January	NNP
10_1101-436634	104	19	5	5	CD
10_1101-436634	104	20	,	,	,
10_1101-436634	104	21	2021	2021	CD
10_1101-436634	104	22	.	.	.
10_1101-436634	104	23	;	;	:
10_1101-436634	104	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	104	25	:	:	:
10_1101-436634	104	26	bioRxiv	biorxiv	VB
10_1101-436634	104	27	preprint	preprint	NN
10_1101-436634	104	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	104	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NNP
10_1101-436634	104	30	6	6	CD
10_1101-436634	104	31	associated	associate	VBN
10_1101-436634	104	32	with	with	IN
10_1101-436634	104	33	a	a	DT
10_1101-436634	104	34	variant	variant	NN
10_1101-436634	104	35	therefore	therefore	RB
10_1101-436634	104	36	may	may	MD
10_1101-436634	104	37	not	not	RB
10_1101-436634	104	38	be	be	VB
10_1101-436634	104	39	completely	completely	RB
10_1101-436634	104	40	describing	describe	VBG
10_1101-436634	104	41	the	the	DT
10_1101-436634	104	42	effect	effect	NN
10_1101-436634	104	43	of	of	IN
10_1101-436634	104	44	the	the	DT
10_1101-436634	104	45	variant	variant	NN
10_1101-436634	104	46	in	in	IN
10_1101-436634	104	47	question	question	NN
10_1101-436634	104	48	in	in	IN
10_1101-436634	104	49	up	up	IN
10_1101-436634	104	50	to	to	IN
10_1101-436634	104	51	~27	~27	.
10_1101-436634	104	52	%	%	NN
10_1101-436634	104	53	of	of	IN
10_1101-436634	104	54	cases	case	NNS
10_1101-436634	104	55	.	.	.
10_1101-436634	105	1	RegTools	RegTools	NNP
10_1101-436634	105	2	identifies	identifies	NNP
10_1101-436634	105	3	splice	splice	NN
10_1101-436634	105	4	altering	alter	VBG
10_1101-436634	105	5	variants	variant	NNS
10_1101-436634	105	6	missed	miss	VBN
10_1101-436634	105	7	by	by	IN
10_1101-436634	105	8	other	other	JJ
10_1101-436634	105	9	splice	splice	NN
10_1101-436634	105	10	variant	variant	JJ
10_1101-436634	105	11	predictors	predictor	NNS
10_1101-436634	105	12	and	and	CC
10_1101-436634	105	13	annotators	annotator	NNS
10_1101-436634	105	14	To	to	TO
10_1101-436634	105	15	evaluate	evaluate	VB
10_1101-436634	105	16	the	the	DT
10_1101-436634	105	17	performance	performance	NN
10_1101-436634	105	18	of	of	IN
10_1101-436634	105	19	RegTools	RegTools	NNP
10_1101-436634	105	20	,	,	,
10_1101-436634	105	21	we	-PRON-	PRP
10_1101-436634	105	22	compared	compare	VBD
10_1101-436634	105	23	our	-PRON-	PRP$
10_1101-436634	105	24	results	result	NNS
10_1101-436634	105	25	to	to	IN
10_1101-436634	105	26	those	those	DT
10_1101-436634	105	27	of	of	IN
10_1101-436634	105	28	SAVNet	SAVNet	NNP
10_1101-436634	105	29	,	,	,
10_1101-436634	105	30	MiSplice	MiSplice	NNP
10_1101-436634	105	31	,	,	,
10_1101-436634	105	32	Veridical	Veridical	NNP
10_1101-436634	105	33	,	,	,
10_1101-436634	105	34	VEP	VEP	NNP
10_1101-436634	105	35	,	,	,
10_1101-436634	105	36	and	and	CC
10_1101-436634	105	37	SpliceAI13,20,21,23,25	SpliceAI13,20,21,23,25	NNP
10_1101-436634	105	38	.	.	.
10_1101-436634	106	1	These	these	DT
10_1101-436634	106	2	tools	tool	NNS
10_1101-436634	106	3	vary	vary	VBP
10_1101-436634	106	4	in	in	IN
10_1101-436634	106	5	their	-PRON-	PRP$
10_1101-436634	106	6	inputs	input	NNS
10_1101-436634	106	7	and	and	CC
10_1101-436634	106	8	methodology	methodology	NN
10_1101-436634	106	9	for	for	IN
10_1101-436634	106	10	identifying	identify	VBG
10_1101-436634	106	11	splice	splice	NN
10_1101-436634	106	12	altering	alter	VBG
10_1101-436634	106	13	variants	variant	NNS
10_1101-436634	106	14	(	(	-LRB-
10_1101-436634	106	15	Figure	Figure	NNP
10_1101-436634	106	16	4A	4A	NNP
10_1101-436634	106	17	)	)	-RRB-
10_1101-436634	106	18	.	.	.
10_1101-436634	107	1	Both	both	CC
10_1101-436634	107	2	VEP	VEP	NNP
10_1101-436634	107	3	and	and	CC
10_1101-436634	107	4	SpliceAI	SpliceAI	VBN
10_1101-436634	107	5	only	only	RB
10_1101-436634	107	6	consider	consider	VB
10_1101-436634	107	7	information	information	NN
10_1101-436634	107	8	about	about	IN
10_1101-436634	107	9	the	the	DT
10_1101-436634	107	10	variant	variant	JJ
10_1101-436634	107	11	and	and	CC
10_1101-436634	107	12	its	-PRON-	PRP$
10_1101-436634	107	13	genomic	genomic	JJ
10_1101-436634	107	14	sequence	sequence	NN
10_1101-436634	107	15	context	context	NN
10_1101-436634	107	16	and	and	CC
10_1101-436634	107	17	do	do	VBP
10_1101-436634	107	18	not	not	RB
10_1101-436634	107	19	consider	consider	VB
10_1101-436634	107	20	information	information	NN
10_1101-436634	107	21	from	from	IN
10_1101-436634	107	22	a	a	DT
10_1101-436634	107	23	sample	sample	NN
10_1101-436634	107	24	’s	’s	,
10_1101-436634	107	25	transcriptome	transcriptome	JJS
10_1101-436634	107	26	.	.	.
10_1101-436634	108	1	A	a	DT
10_1101-436634	108	2	variant	variant	NN
10_1101-436634	108	3	is	be	VBZ
10_1101-436634	108	4	considered	consider	VBN
10_1101-436634	108	5	to	to	TO
10_1101-436634	108	6	be	be	VB
10_1101-436634	108	7	splice	splice	NN
10_1101-436634	108	8	relevant	relevant	JJ
10_1101-436634	108	9	according	accord	VBG
10_1101-436634	108	10	to	to	IN
10_1101-436634	108	11	VEP	VEP	NNP
10_1101-436634	108	12	if	if	IN
10_1101-436634	108	13	it	-PRON-	PRP
10_1101-436634	108	14	occurs	occur	VBZ
10_1101-436634	108	15	within	within	IN
10_1101-436634	108	16	1	1	CD
10_1101-436634	108	17	-	-	SYM
10_1101-436634	108	18	3	3	CD
10_1101-436634	108	19	bases	basis	NNS
10_1101-436634	108	20	on	on	IN
10_1101-436634	108	21	the	the	DT
10_1101-436634	108	22	exonic	exonic	JJ
10_1101-436634	108	23	side	side	NN
10_1101-436634	108	24	or	or	CC
10_1101-436634	108	25	1	1	CD
10_1101-436634	108	26	-	-	SYM
10_1101-436634	108	27	8	8	CD
10_1101-436634	108	28	bases	basis	NNS
10_1101-436634	108	29	on	on	IN
10_1101-436634	108	30	the	the	DT
10_1101-436634	108	31	intronic	intronic	JJ
10_1101-436634	108	32	side	side	NN
10_1101-436634	108	33	of	of	IN
10_1101-436634	108	34	a	a	DT
10_1101-436634	108	35	splice	splice	NN
10_1101-436634	108	36	site	site	NN
10_1101-436634	108	37	.	.	.
10_1101-436634	109	1	SpliceAI	SpliceAI	VBN
10_1101-436634	109	2	does	do	VBZ
10_1101-436634	109	3	not	not	RB
10_1101-436634	109	4	have	have	VB
10_1101-436634	109	5	restrictions	restriction	NNS
10_1101-436634	109	6	on	on	IN
10_1101-436634	109	7	where	where	WRB
10_1101-436634	109	8	the	the	DT
10_1101-436634	109	9	variant	variant	NN
10_1101-436634	109	10	can	can	MD
10_1101-436634	109	11	occur	occur	VB
10_1101-436634	109	12	in	in	IN
10_1101-436634	109	13	relation	relation	NN
10_1101-436634	109	14	to	to	IN
10_1101-436634	109	15	the	the	DT
10_1101-436634	109	16	splice	splice	NN
10_1101-436634	109	17	site	site	NN
10_1101-436634	109	18	but	but	CC
10_1101-436634	109	19	by	by	IN
10_1101-436634	109	20	default	default	NN
10_1101-436634	109	21	,	,	,
10_1101-436634	109	22	it	-PRON-	PRP
10_1101-436634	109	23	predicts	predict	VBZ
10_1101-436634	109	24	one	one	CD
10_1101-436634	109	25	new	new	JJ
10_1101-436634	109	26	donor	donor	NN
10_1101-436634	109	27	and	and	CC
10_1101-436634	109	28	acceptor	acceptor	NN
10_1101-436634	109	29	site	site	NN
10_1101-436634	109	30	within	within	IN
10_1101-436634	109	31	50	50	CD
10_1101-436634	109	32	bp	bp	NN
10_1101-436634	109	33	of	of	IN
10_1101-436634	109	34	the	the	DT
10_1101-436634	109	35	variant	variant	NN
10_1101-436634	109	36	,	,	,
10_1101-436634	109	37	based	base	VBN
10_1101-436634	109	38	on	on	IN
10_1101-436634	109	39	reference	reference	NN
10_1101-436634	109	40	transcript	transcript	NN
10_1101-436634	109	41	sequences	sequence	NNS
10_1101-436634	109	42	from	from	IN
10_1101-436634	109	43	GENCODE	GENCODE	NNP
10_1101-436634	109	44	.	.	.
10_1101-436634	110	1	Like	like	IN
10_1101-436634	110	2	RegTools	RegTools	NNP
10_1101-436634	110	3	,	,	,
10_1101-436634	110	4	SAVNet	SAVNet	NNP
10_1101-436634	110	5	,	,	,
10_1101-436634	110	6	MiSplice	MiSplice	NNP
10_1101-436634	110	7	,	,	,
10_1101-436634	110	8	and	and	CC
10_1101-436634	110	9	Veridical	veridical	JJ
10_1101-436634	110	10	integrate	integrate	VB
10_1101-436634	110	11	genomic	genomic	JJ
10_1101-436634	110	12	and	and	CC
10_1101-436634	110	13	transcriptomic	transcriptomic	JJ
10_1101-436634	110	14	data	datum	NNS
10_1101-436634	110	15	in	in	IN
10_1101-436634	110	16	order	order	NN
10_1101-436634	110	17	to	to	TO
10_1101-436634	110	18	identify	identify	VB
10_1101-436634	110	19	splice	splice	NN
10_1101-436634	110	20	altering	altering	NN
10_1101-436634	110	21	variants	variant	NNS
10_1101-436634	110	22	.	.	.
10_1101-436634	111	1	MiSplice	MiSplice	NNP
10_1101-436634	111	2	only	only	RB
10_1101-436634	111	3	considers	consider	VBZ
10_1101-436634	111	4	junctions	junction	NNS
10_1101-436634	111	5	that	that	WDT
10_1101-436634	111	6	occur	occur	VBP
10_1101-436634	111	7	within	within	IN
10_1101-436634	111	8	20	20	CD
10_1101-436634	111	9	bp	bp	NN
10_1101-436634	111	10	of	of	IN
10_1101-436634	111	11	the	the	DT
10_1101-436634	111	12	variant	variant	NN
10_1101-436634	111	13	.	.	.
10_1101-436634	112	1	Additionally	additionally	RB
10_1101-436634	112	2	,	,	,
10_1101-436634	112	3	SAVNet	SAVNet	NNP
10_1101-436634	112	4	,	,	,
10_1101-436634	112	5	MiSplice	MiSplice	NNP
10_1101-436634	112	6	,	,	,
10_1101-436634	112	7	and	and	CC
10_1101-436634	112	8	Veridical	veridical	JJ
10_1101-436634	112	9	filter	filter	NN
10_1101-436634	112	10	out	out	RP
10_1101-436634	112	11	any	any	DT
10_1101-436634	112	12	transcripts	transcript	NNS
10_1101-436634	112	13	found	find	VBN
10_1101-436634	112	14	within	within	IN
10_1101-436634	112	15	the	the	DT
10_1101-436634	112	16	reference	reference	NN
10_1101-436634	112	17	transcriptome	transcriptome	VBN
10_1101-436634	112	18	.	.	.
10_1101-436634	113	1	SAVNet	SAVNet	NNP
10_1101-436634	113	2	,	,	,
10_1101-436634	113	3	MiSplice	MiSplice	NNP
10_1101-436634	113	4	,	,	,
10_1101-436634	113	5	and	and	CC
10_1101-436634	113	6	Veridical	veridical	JJ
10_1101-436634	113	7	employ	employ	JJ
10_1101-436634	113	8	different	different	JJ
10_1101-436634	113	9	statistical	statistical	JJ
10_1101-436634	113	10	methods	method	NNS
10_1101-436634	113	11	for	for	IN
10_1101-436634	113	12	the	the	DT
10_1101-436634	113	13	identification	identification	NN
10_1101-436634	113	14	of	of	IN
10_1101-436634	113	15	splice	splice	NN
10_1101-436634	113	16	altering	altering	NN
10_1101-436634	113	17	variants	variant	NNS
10_1101-436634	113	18	.	.	.
10_1101-436634	114	1	In	in	IN
10_1101-436634	114	2	contrast	contrast	NN
10_1101-436634	114	3	to	to	IN
10_1101-436634	114	4	RegTools	RegTools	NNP
10_1101-436634	114	5	,	,	,
10_1101-436634	114	6	none	none	NN
10_1101-436634	114	7	of	of	IN
10_1101-436634	114	8	the	the	DT
10_1101-436634	114	9	mentioned	mention	VBN
10_1101-436634	114	10	tools	tool	NNS
10_1101-436634	114	11	allow	allow	VBP
10_1101-436634	114	12	the	the	DT
10_1101-436634	114	13	user	user	NN
10_1101-436634	114	14	to	to	TO
10_1101-436634	114	15	set	set	VB
10_1101-436634	114	16	a	a	DT
10_1101-436634	114	17	custom	custom	NN
10_1101-436634	114	18	window	window	NN
10_1101-436634	114	19	in	in	IN
10_1101-436634	114	20	which	which	WDT
10_1101-436634	114	21	they	-PRON-	PRP
10_1101-436634	114	22	wish	wish	VBP
10_1101-436634	114	23	to	to	TO
10_1101-436634	114	24	focus	focus	VB
10_1101-436634	114	25	splice	splice	NN
10_1101-436634	114	26	altering	alter	VBG
10_1101-436634	114	27	variant	variant	JJ
10_1101-436634	114	28	discovery	discovery	NN
10_1101-436634	114	29	(	(	-LRB-
10_1101-436634	114	30	e.g.	e.g.	RB
10_1101-436634	115	1	around	around	IN
10_1101-436634	115	2	the	the	DT
10_1101-436634	115	3	splice	splice	NN
10_1101-436634	115	4	site	site	NN
10_1101-436634	115	5	,	,	,
10_1101-436634	115	6	all	all	DT
10_1101-436634	115	7	exonic	exonic	JJ
10_1101-436634	115	8	variants	variant	NNS
10_1101-436634	115	9	,	,	,
10_1101-436634	115	10	etc	etc	FW
10_1101-436634	115	11	.	.	.
10_1101-436634	115	12	)	)	-RRB-
10_1101-436634	115	13	.	.	.
10_1101-436634	116	1	These	these	DT
10_1101-436634	116	2	tools	tool	NNS
10_1101-436634	116	3	have	have	VBP
10_1101-436634	116	4	different	different	JJ
10_1101-436634	116	5	levels	level	NNS
10_1101-436634	116	6	of	of	IN
10_1101-436634	116	7	code	code	NN
10_1101-436634	116	8	availability	availability	NN
10_1101-436634	116	9	.	.	.
10_1101-436634	117	1	MiSplice	MiSplice	NNP
10_1101-436634	117	2	is	be	VBZ
10_1101-436634	117	3	available	available	JJ
10_1101-436634	117	4	via	via	IN
10_1101-436634	117	5	GitHub	GitHub	NNP
10_1101-436634	117	6	as	as	IN
10_1101-436634	117	7	a	a	DT
10_1101-436634	117	8	collection	collection	NN
10_1101-436634	117	9	of	of	IN
10_1101-436634	117	10	Perl	Perl	NNP
10_1101-436634	117	11	scripts	script	NNS
10_1101-436634	117	12	that	that	WDT
10_1101-436634	117	13	are	be	VBP
10_1101-436634	117	14	built	build	VBN
10_1101-436634	117	15	to	to	TO
10_1101-436634	117	16	run	run	VB
10_1101-436634	117	17	via	via	IN
10_1101-436634	117	18	Load	Load	NNP
10_1101-436634	117	19	Sharing	Sharing	NNP
10_1101-436634	117	20	Facility	Facility	NNP
10_1101-436634	117	21	(	(	-LRB-
10_1101-436634	117	22	LSF	LSF	NNP
10_1101-436634	117	23	)	)	-RRB-
10_1101-436634	117	24	job	job	NN
10_1101-436634	117	25	scheduling	scheduling	NN
10_1101-436634	117	26	.	.	.
10_1101-436634	118	1	To	to	TO
10_1101-436634	118	2	run	run	VB
10_1101-436634	118	3	MiSplice	MiSplice	NNP
10_1101-436634	118	4	without	without	IN
10_1101-436634	118	5	an	an	DT
10_1101-436634	118	6	LSF	LSF	NNP
10_1101-436634	118	7	cluster	cluster	NN
10_1101-436634	118	8	,	,	,
10_1101-436634	118	9	the	the	DT
10_1101-436634	118	10	authors	author	NNS
10_1101-436634	118	11	mention	mention	VBP
10_1101-436634	118	12	code	code	NN
10_1101-436634	118	13	changes	change	NNS
10_1101-436634	118	14	are	be	VBP
10_1101-436634	118	15	required	require	VBN
10_1101-436634	118	16	.	.	.
10_1101-436634	119	1	Veridical	veridical	JJ
10_1101-436634	119	2	is	be	VBZ
10_1101-436634	119	3	available	available	JJ
10_1101-436634	119	4	via	via	IN
10_1101-436634	119	5	a	a	DT
10_1101-436634	119	6	subscription	subscription	NN
10_1101-436634	119	7	through	through	IN
10_1101-436634	119	8	CytoGnomix	CytoGnomix	NNP
10_1101-436634	119	9	’s	’s	POS
10_1101-436634	119	10	MutationForecaster	MutationForecaster	NNP
10_1101-436634	119	11	.	.	.
10_1101-436634	120	1	Similar	similar	JJ
10_1101-436634	120	2	to	to	IN
10_1101-436634	120	3	RegTools	RegTools	NNP
10_1101-436634	120	4	,	,	,
10_1101-436634	120	5	SAVNet	SAVNet	NNP
10_1101-436634	120	6	is	be	VBZ
10_1101-436634	120	7	available	available	JJ
10_1101-436634	120	8	via	via	IN
10_1101-436634	120	9	GitHub	GitHub	NNP
10_1101-436634	120	10	or	or	CC
10_1101-436634	120	11	through	through	IN
10_1101-436634	120	12	a	a	DT
10_1101-436634	120	13	Docker	Docker	NNP
10_1101-436634	120	14	image	image	NN
10_1101-436634	120	15	.	.	.
10_1101-436634	121	1	However	however	RB
10_1101-436634	121	2	,	,	,
10_1101-436634	121	3	SAVNet	SAVNet	NNP
10_1101-436634	121	4	relies	rely	VBZ
10_1101-436634	121	5	on	on	IN
10_1101-436634	121	6	splicing	splicing	NN
10_1101-436634	121	7	junction	junction	NN
10_1101-436634	121	8	files	file	NNS
10_1101-436634	121	9	generated	generate	VBN
10_1101-436634	121	10	by	by	IN
10_1101-436634	121	11	STAR29	STAR29	NNP
10_1101-436634	121	12	whereas	whereas	IN
10_1101-436634	121	13	RegTools	regtool	NNS
10_1101-436634	121	14	can	can	MD
10_1101-436634	121	15	use	use	VB
10_1101-436634	121	16	RNA	RNA	NNP
10_1101-436634	121	17	-	-	HYPH
10_1101-436634	121	18	Seq	seq	NN
10_1101-436634	121	19	alignment	alignment	NN
10_1101-436634	121	20	files	file	NNS
10_1101-436634	121	21	from	from	IN
10_1101-436634	121	22	HISAT230	HISAT230	NNP
10_1101-436634	121	23	,	,	,
10_1101-436634	121	24	TopHat231	TopHat231	NNP
10_1101-436634	121	25	,	,	,
10_1101-436634	121	26	or	or	CC
10_1101-436634	121	27	STAR	STAR	NNP
10_1101-436634	121	28	,	,	,
10_1101-436634	121	29	thus	thus	RB
10_1101-436634	121	30	allowing	allow	VBG
10_1101-436634	121	31	it	-PRON-	PRP
10_1101-436634	121	32	to	to	TO
10_1101-436634	121	33	be	be	VB
10_1101-436634	121	34	integrated	integrate	VBN
10_1101-436634	121	35	into	into	IN
10_1101-436634	121	36	bioinformatic	bioinformatic	JJ
10_1101-436634	121	37	workflows	workflow	NNS
10_1101-436634	121	38	more	more	RBR
10_1101-436634	121	39	easily	easily	RB
10_1101-436634	121	40	.	.	.
10_1101-436634	122	1	In	in	IN
10_1101-436634	122	2	their	-PRON-	PRP$
10_1101-436634	122	3	recent	recent	JJ
10_1101-436634	122	4	publications	publication	NNS
10_1101-436634	122	5	,	,	,
10_1101-436634	122	6	SAVNet23	SAVNet23	NNP
10_1101-436634	122	7	,	,	,
10_1101-436634	122	8	MiSplice20	MiSplice20	NNP
10_1101-436634	122	9	,	,	,
10_1101-436634	122	10	and	and	CC
10_1101-436634	122	11	Veridical21,22	Veridical21,22	NNP
10_1101-436634	122	12	also	also	RB
10_1101-436634	122	13	analyzed	analyze	VBD
10_1101-436634	122	14	data	datum	NNS
10_1101-436634	122	15	from	from	IN
10_1101-436634	122	16	TCGA	TCGA	NNP
10_1101-436634	122	17	,	,	,
10_1101-436634	122	18	with	with	IN
10_1101-436634	122	19	only	only	JJ
10_1101-436634	122	20	minor	minor	JJ
10_1101-436634	122	21	differences	difference	NNS
10_1101-436634	122	22	in	in	IN
10_1101-436634	122	23	the	the	DT
10_1101-436634	122	24	number	number	NN
10_1101-436634	122	25	of	of	IN
10_1101-436634	122	26	samples	sample	NNS
10_1101-436634	122	27	included	include	VBN
10_1101-436634	122	28	for	for	IN
10_1101-436634	122	29	each	each	DT
10_1101-436634	122	30	study	study	NN
10_1101-436634	122	31	.	.	.
10_1101-436634	123	1	VEP	VEP	NNP
10_1101-436634	123	2	and	and	CC
10_1101-436634	123	3	SpliceAI	spliceai	JJ
10_1101-436634	123	4	results	result	NNS
10_1101-436634	123	5	were	be	VBD
10_1101-436634	123	6	obtained	obtain	VBN
10_1101-436634	123	7	by	by	IN
10_1101-436634	123	8	running	run	VBG
10_1101-436634	123	9	each	each	DT
10_1101-436634	123	10	tool	tool	NN
10_1101-436634	123	11	on	on	IN
10_1101-436634	123	12	all	all	DT
10_1101-436634	123	13	starting	start	VBG
10_1101-436634	123	14	variants	variant	NNS
10_1101-436634	123	15	for	for	IN
10_1101-436634	123	16	the	the	DT
10_1101-436634	123	17	35	35	CD
10_1101-436634	123	18	cohorts	cohort	NNS
10_1101-436634	123	19	included	include	VBN
10_1101-436634	123	20	in	in	IN
10_1101-436634	123	21	this	this	DT
10_1101-436634	123	22	study	study	NN
10_1101-436634	123	23	.	.	.
10_1101-436634	124	1	In	in	IN
10_1101-436634	124	2	order	order	NN
10_1101-436634	124	3	to	to	TO
10_1101-436634	124	4	efficiently	efficiently	RB
10_1101-436634	124	5	compare	compare	VB
10_1101-436634	124	6	this	this	DT
10_1101-436634	124	7	data	data	NN
10_1101-436634	124	8	,	,	,
10_1101-436634	124	9	an	an	DT
10_1101-436634	124	10	UpSet	UpSet	NNP
10_1101-436634	124	11	plot	plot	NN
10_1101-436634	124	12	(	(	-LRB-
10_1101-436634	124	13	Figure	figure	NN
10_1101-436634	124	14	4B	4b	NN
10_1101-436634	124	15	)	)	-RRB-
10_1101-436634	124	16	was	be	VBD
10_1101-436634	124	17	created32	created32	VBN
10_1101-436634	124	18	.	.	.
10_1101-436634	125	1	Only	only	RB
10_1101-436634	125	2	343	343	CD
10_1101-436634	125	3	variants	variant	NNS
10_1101-436634	125	4	are	be	VBP
10_1101-436634	125	5	identified	identify	VBN
10_1101-436634	125	6	as	as	IN
10_1101-436634	125	7	splice	splice	NN
10_1101-436634	125	8	altering	alter	VBG
10_1101-436634	125	9	by	by	IN
10_1101-436634	125	10	all	all	DT
10_1101-436634	125	11	six	six	CD
10_1101-436634	125	12	tools	tool	NNS
10_1101-436634	125	13	.	.	.
10_1101-436634	126	1	Comparatively	comparatively	RB
10_1101-436634	126	2	,	,	,
10_1101-436634	126	3	MiSplice	MiSplice	NNP
10_1101-436634	126	4	and	and	CC
10_1101-436634	126	5	SAVNet	SAVNet	NNP
10_1101-436634	126	6	find	find	VBP
10_1101-436634	126	7	few	few	JJ
10_1101-436634	126	8	splice	splice	NN
10_1101-436634	126	9	altering	alter	VBG
10_1101-436634	126	10	variants	variant	NNS
10_1101-436634	126	11	,	,	,
10_1101-436634	126	12	potentially	potentially	RB
10_1101-436634	126	13	indicating	indicate	VBG
10_1101-436634	126	14	that	that	IN
10_1101-436634	126	15	these	these	DT
10_1101-436634	126	16	tools	tool	NNS
10_1101-436634	126	17	are	be	VBP
10_1101-436634	126	18	overlooking	overlook	VBG
10_1101-436634	126	19	the	the	DT
10_1101-436634	126	20	complete	complete	JJ
10_1101-436634	126	21	set	set	NN
10_1101-436634	126	22	of	of	IN
10_1101-436634	126	23	variants	variant	NNS
10_1101-436634	126	24	that	that	WDT
10_1101-436634	126	25	have	have	VBP
10_1101-436634	126	26	an	an	DT
10_1101-436634	126	27	effect	effect	NN
10_1101-436634	126	28	on	on	IN
10_1101-436634	126	29	splicing	splicing	NN
10_1101-436634	126	30	.	.	.
10_1101-436634	127	1	In	in	IN
10_1101-436634	127	2	contrast	contrast	NN
10_1101-436634	127	3	,	,	,
10_1101-436634	127	4	Veridical	veridical	JJ
10_1101-436634	127	5	identifies	identifie	NNS
10_1101-436634	127	6	by	by	IN
10_1101-436634	127	7	far	far	RB
10_1101-436634	127	8	the	the	DT
10_1101-436634	127	9	most	most	JJS
10_1101-436634	127	10	splice	splice	NN
10_1101-436634	127	11	altering	alter	VBG
10_1101-436634	127	12	variants	variant	NNS
10_1101-436634	127	13	across	across	IN
10_1101-436634	127	14	all	all	DT
10_1101-436634	127	15	tools	tool	NNS
10_1101-436634	127	16	,	,	,
10_1101-436634	127	17	with	with	IN
10_1101-436634	127	18	94.54	94.54	CD
10_1101-436634	127	19	percent	percent	NN
10_1101-436634	127	20	of	of	IN
10_1101-436634	127	21	its	-PRON-	PRP$
10_1101-436634	127	22	calls	call	NNS
10_1101-436634	127	23	being	be	VBG
10_1101-436634	127	24	found	find	VBN
10_1101-436634	127	25	by	by	IN
10_1101-436634	127	26	it	-PRON-	PRP
10_1101-436634	127	27	alone	alone	RB
10_1101-436634	127	28	.	.	.
10_1101-436634	128	1	SpliceAI	SpliceAI	VBN
10_1101-436634	128	2	and	and	CC
10_1101-436634	128	3	VEP	VEP	NNP
10_1101-436634	128	4	called	call	VBD
10_1101-436634	128	5	a	a	DT
10_1101-436634	128	6	large	large	JJ
10_1101-436634	128	7	number	number	NN
10_1101-436634	128	8	of	of	IN
10_1101-436634	128	9	variants	variant	NNS
10_1101-436634	128	10	,	,	,
10_1101-436634	128	11	either	either	CC
10_1101-436634	128	12	alone	alone	RB
10_1101-436634	128	13	or	or	CC
10_1101-436634	128	14	in	in	IN
10_1101-436634	128	15	agreement	agreement	NN
10_1101-436634	128	16	,	,	,
10_1101-436634	128	17	that	that	IN
10_1101-436634	128	18	none	none	NN
10_1101-436634	128	19	of	of	IN
10_1101-436634	128	20	the	the	DT
10_1101-436634	128	21	tools	tool	NNS
10_1101-436634	128	22	that	that	WDT
10_1101-436634	128	23	integrate	integrate	VBP
10_1101-436634	128	24	transcriptomic	transcriptomic	JJ
10_1101-436634	128	25	data	datum	NNS
10_1101-436634	128	26	from	from	IN
10_1101-436634	128	27	samples	sample	NNS
10_1101-436634	128	28	identify	identify	VBP
10_1101-436634	128	29	.	.	.
10_1101-436634	129	1	This	this	DT
10_1101-436634	129	2	highlights	highlight	VBZ
10_1101-436634	129	3	a	a	DT
10_1101-436634	129	4	limitation	limitation	NN
10_1101-436634	129	5	of	of	IN
10_1101-436634	129	6	using	use	VBG
10_1101-436634	129	7	tools	tool	NNS
10_1101-436634	129	8	that	that	WDT
10_1101-436634	129	9	only	only	RB
10_1101-436634	129	10	focus	focus	VBP
10_1101-436634	129	11	on	on	IN
10_1101-436634	129	12	genomic	genomic	JJ
10_1101-436634	129	13	data	datum	NNS
10_1101-436634	129	14	,	,	,
10_1101-436634	129	15	particularly	particularly	RB
10_1101-436634	129	16	in	in	IN
10_1101-436634	129	17	a	a	DT
10_1101-436634	129	18	disease	disease	NN
10_1101-436634	129	19	context	context	NN
10_1101-436634	129	20	where	where	WRB
10_1101-436634	129	21	transcripts	transcript	NNS
10_1101-436634	129	22	are	be	VBP
10_1101-436634	129	23	unlikely	unlikely	JJ
10_1101-436634	129	24	to	to	TO
10_1101-436634	129	25	have	have	VB
10_1101-436634	129	26	been	be	VBN
10_1101-436634	129	27	annotated	annotate	VBN
10_1101-436634	129	28	before	before	RB
10_1101-436634	129	29	.	.	.
10_1101-436634	130	1	RegTools	RegTools	NNP
10_1101-436634	130	2	addresses	address	VBZ
10_1101-436634	130	3	these	these	DT
10_1101-436634	130	4	short	short	JJ
10_1101-436634	130	5	-	-	HYPH
10_1101-436634	130	6	comings	coming	NNS
10_1101-436634	130	7	by	by	IN
10_1101-436634	130	8	identifying	identify	VBG
10_1101-436634	130	9	what	what	WP
10_1101-436634	130	10	pieces	piece	NNS
10_1101-436634	130	11	of	of	IN
10_1101-436634	130	12	information	information	NN
10_1101-436634	130	13	to	to	TO
10_1101-436634	130	14	extract	extract	VB
10_1101-436634	130	15	from	from	IN
10_1101-436634	130	16	a	a	DT
10_1101-436634	130	17	sample	sample	NN
10_1101-436634	130	18	’s	’s	,
10_1101-436634	130	19	genome	genome	NN
10_1101-436634	130	20	and	and	CC
10_1101-436634	130	21	transcriptome	transcriptome	VBP
10_1101-436634	130	22	in	in	IN
10_1101-436634	130	23	a	a	DT
10_1101-436634	130	24	very	very	RB
10_1101-436634	130	25	basic	basic	JJ
10_1101-436634	130	26	,	,	,
10_1101-436634	130	27	unbiased	unbiased	JJ
10_1101-436634	130	28	way	way	NN
10_1101-436634	130	29	that	that	WDT
10_1101-436634	130	30	allows	allow	VBZ
10_1101-436634	130	31	for	for	IN
10_1101-436634	130	32	generalization	generalization	NN
10_1101-436634	130	33	.	.	.
10_1101-436634	131	1	Other	other	JJ
10_1101-436634	131	2	.CC	.CC	NFP
10_1101-436634	131	3	-	-	HYPH
10_1101-436634	131	4	BY	by	IN
10_1101-436634	131	5	-	-	HYPH
10_1101-436634	131	6	NC	NC	NNP
10_1101-436634	131	7	-	-	HYPH
10_1101-436634	131	8	ND	ND	NNP
10_1101-436634	131	9	4.0	4.0	CD
10_1101-436634	131	10	International	international	JJ
10_1101-436634	131	11	licensea	licensea	NNS
10_1101-436634	131	12	certified	certify	VBN
10_1101-436634	131	13	by	by	IN
10_1101-436634	131	14	peer	peer	NN
10_1101-436634	131	15	review	review	NN
10_1101-436634	131	16	)	)	-RRB-
10_1101-436634	131	17	is	be	VBZ
10_1101-436634	131	18	the	the	DT
10_1101-436634	131	19	author	author	NN
10_1101-436634	131	20	/	/	SYM
10_1101-436634	131	21	funder	funder	NN
10_1101-436634	131	22	,	,	,
10_1101-436634	131	23	who	who	WP
10_1101-436634	131	24	has	have	VBZ
10_1101-436634	131	25	granted	grant	VBN
10_1101-436634	131	26	bioRxiv	biorxiv	IN
10_1101-436634	131	27	a	a	DT
10_1101-436634	131	28	license	license	NN
10_1101-436634	131	29	to	to	TO
10_1101-436634	131	30	display	display	VB
10_1101-436634	131	31	the	the	DT
10_1101-436634	131	32	preprint	preprint	NN
10_1101-436634	131	33	in	in	IN
10_1101-436634	131	34	perpetuity	perpetuity	NN
10_1101-436634	131	35	.	.	.
10_1101-436634	132	1	It	-PRON-	PRP
10_1101-436634	132	2	is	be	VBZ
10_1101-436634	132	3	made	make	VBN
10_1101-436634	132	4	available	available	JJ
10_1101-436634	132	5	under	under	IN
10_1101-436634	132	6	The	the	DT
10_1101-436634	132	7	copyright	copyright	NN
10_1101-436634	132	8	holder	holder	NN
10_1101-436634	132	9	for	for	IN
10_1101-436634	132	10	this	this	DT
10_1101-436634	132	11	preprint	preprint	NN
10_1101-436634	132	12	(	(	-LRB-
10_1101-436634	132	13	which	which	WDT
10_1101-436634	132	14	was	be	VBD
10_1101-436634	132	15	notthis	notthis	DT
10_1101-436634	132	16	version	version	NN
10_1101-436634	132	17	posted	post	VBN
10_1101-436634	132	18	January	January	NNP
10_1101-436634	132	19	5	5	CD
10_1101-436634	132	20	,	,	,
10_1101-436634	132	21	2021	2021	CD
10_1101-436634	132	22	.	.	.
10_1101-436634	132	23	;	;	:
10_1101-436634	132	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	132	25	:	:	:
10_1101-436634	132	26	bioRxiv	biorxiv	VB
10_1101-436634	132	27	preprint	preprint	NN
10_1101-436634	132	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	132	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	132	30	7	7	CD
10_1101-436634	132	31	tools	tool	NNS
10_1101-436634	132	32	either	either	CC
10_1101-436634	132	33	only	only	RB
10_1101-436634	132	34	analyze	analyze	VB
10_1101-436634	132	35	genomic	genomic	JJ
10_1101-436634	132	36	data	datum	NNS
10_1101-436634	132	37	,	,	,
10_1101-436634	132	38	focus	focus	VBP
10_1101-436634	132	39	on	on	IN
10_1101-436634	132	40	junctions	junction	NNS
10_1101-436634	132	41	where	where	WRB
10_1101-436634	132	42	either	either	CC
10_1101-436634	132	43	the	the	DT
10_1101-436634	132	44	canonical	canonical	JJ
10_1101-436634	132	45	donor	donor	NN
10_1101-436634	132	46	or	or	CC
10_1101-436634	132	47	acceptor	acceptor	NN
10_1101-436634	132	48	site	site	NN
10_1101-436634	132	49	is	be	VBZ
10_1101-436634	132	50	affected	affect	VBN
10_1101-436634	132	51	(	(	-LRB-
10_1101-436634	132	52	missing	miss	VBG
10_1101-436634	132	53	junctions	junction	NNS
10_1101-436634	132	54	that	that	WDT
10_1101-436634	132	55	result	result	VBP
10_1101-436634	132	56	from	from	IN
10_1101-436634	132	57	complete	complete	JJ
10_1101-436634	132	58	exon	exon	JJ
10_1101-436634	132	59	skipping	skipping	NN
10_1101-436634	132	60	)	)	-RRB-
10_1101-436634	132	61	,	,	,
10_1101-436634	132	62	or	or	CC
10_1101-436634	132	63	consider	consider	VB
10_1101-436634	132	64	only	only	RB
10_1101-436634	132	65	those	those	DT
10_1101-436634	132	66	variants	variant	NNS
10_1101-436634	132	67	within	within	IN
10_1101-436634	132	68	a	a	DT
10_1101-436634	132	69	very	very	RB
10_1101-436634	132	70	narrow	narrow	JJ
10_1101-436634	132	71	distance	distance	NN
10_1101-436634	132	72	from	from	IN
10_1101-436634	132	73	known	know	VBN
10_1101-436634	132	74	splice	splice	NN
10_1101-436634	132	75	sites	site	NNS
10_1101-436634	132	76	.	.	.
10_1101-436634	133	1	RegTools	regtool	NNS
10_1101-436634	133	2	can	can	MD
10_1101-436634	133	3	include	include	VB
10_1101-436634	133	4	any	any	DT
10_1101-436634	133	5	kind	kind	NN
10_1101-436634	133	6	of	of	IN
10_1101-436634	133	7	junction	junction	NN
10_1101-436634	133	8	type	type	NN
10_1101-436634	133	9	,	,	,
10_1101-436634	133	10	including	include	VBG
10_1101-436634	133	11	exon	exon	NN
10_1101-436634	133	12	-	-	HYPH
10_1101-436634	133	13	exon	exon	NN
10_1101-436634	133	14	junctions	junction	NNS
10_1101-436634	133	15	that	that	WDT
10_1101-436634	133	16	have	have	VBP
10_1101-436634	133	17	ends	end	NNS
10_1101-436634	133	18	that	that	WDT
10_1101-436634	133	19	are	be	VBP
10_1101-436634	133	20	not	not	RB
10_1101-436634	133	21	known	know	VBN
10_1101-436634	133	22	donor	donor	NN
10_1101-436634	133	23	/	/	SYM
10_1101-436634	133	24	acceptor	acceptor	NN
10_1101-436634	133	25	sites	site	NNS
10_1101-436634	133	26	according	accord	VBG
10_1101-436634	133	27	to	to	IN
10_1101-436634	133	28	the	the	DT
10_1101-436634	133	29	GTF	GTF	NNP
10_1101-436634	133	30	file	file	NN
10_1101-436634	133	31	(	(	-LRB-
10_1101-436634	133	32	N	n	IN
10_1101-436634	133	33	junction	junction	NN
10_1101-436634	133	34	according	accord	VBG
10_1101-436634	133	35	to	to	IN
10_1101-436634	133	36	RegTools	RegTools	NNP
10_1101-436634	133	37	)	)	-RRB-
10_1101-436634	133	38	,	,	,
10_1101-436634	133	39	any	any	DT
10_1101-436634	133	40	distance	distance	NN
10_1101-436634	133	41	size	size	NN
10_1101-436634	133	42	to	to	TO
10_1101-436634	133	43	make	make	VB
10_1101-436634	133	44	variant	variant	JJ
10_1101-436634	133	45	-	-	HYPH
10_1101-436634	133	46	junction	junction	NN
10_1101-436634	133	47	associations	association	NNS
10_1101-436634	133	48	,	,	,
10_1101-436634	133	49	and	and	CC
10_1101-436634	133	50	any	any	DT
10_1101-436634	133	51	window	window	NN
10_1101-436634	133	52	size	size	NN
10_1101-436634	133	53	in	in	IN
10_1101-436634	133	54	which	which	WDT
10_1101-436634	133	55	to	to	TO
10_1101-436634	133	56	consider	consider	VB
10_1101-436634	133	57	variants	variant	NNS
10_1101-436634	133	58	.	.	.
10_1101-436634	134	1	Due	due	IN
10_1101-436634	134	2	to	to	IN
10_1101-436634	134	3	these	these	DT
10_1101-436634	134	4	advantages	advantage	NNS
10_1101-436634	134	5	,	,	,
10_1101-436634	134	6	RegTools	RegTools	NNP
10_1101-436634	134	7	identified	identify	VBN
10_1101-436634	134	8	events	event	NNS
10_1101-436634	134	9	missed	miss	VBN
10_1101-436634	134	10	by	by	IN
10_1101-436634	134	11	one	one	CD
10_1101-436634	134	12	or	or	CC
10_1101-436634	134	13	multiple	multiple	NN
10_1101-436634	134	14	of	of	IN
10_1101-436634	134	15	the	the	DT
10_1101-436634	134	16	tools	tool	NNS
10_1101-436634	134	17	to	to	TO
10_1101-436634	134	18	which	which	WDT
10_1101-436634	134	19	we	-PRON-	PRP
10_1101-436634	134	20	compared	compare	VBD
10_1101-436634	134	21	(	(	-LRB-
10_1101-436634	134	22	Figure	figure	NN
10_1101-436634	134	23	4B	4b	NN
10_1101-436634	134	24	;	;	:
10_1101-436634	134	25	Supplementary	Supplementary	NNP
10_1101-436634	134	26	Figures	Figures	NNPS
10_1101-436634	134	27	4	4	CD
10_1101-436634	134	28	and	and	CC
10_1101-436634	134	29	5	5	CD
10_1101-436634	134	30	)	)	-RRB-
10_1101-436634	134	31	.	.	.
10_1101-436634	135	1	Pan	pan	JJ
10_1101-436634	135	2	-	-	JJ
10_1101-436634	135	3	cancer	cancer	JJ
10_1101-436634	135	4	analysis	analysis	NN
10_1101-436634	135	5	reveals	reveal	VBZ
10_1101-436634	135	6	novel	novel	JJ
10_1101-436634	135	7	splicing	splicing	NN
10_1101-436634	135	8	patterns	pattern	NNS
10_1101-436634	135	9	within	within	IN
10_1101-436634	135	10	known	know	VBN
10_1101-436634	135	11	cancer	cancer	NN
10_1101-436634	135	12	genes	gene	NNS
10_1101-436634	135	13	and	and	CC
10_1101-436634	135	14	potential	potential	JJ
10_1101-436634	135	15	cancer	cancer	NN
10_1101-436634	135	16	drivers	driver	NNS
10_1101-436634	135	17	While	while	IN
10_1101-436634	135	18	efforts	effort	NNS
10_1101-436634	135	19	have	have	VBP
10_1101-436634	135	20	been	be	VBN
10_1101-436634	135	21	made	make	VBN
10_1101-436634	135	22	to	to	TO
10_1101-436634	135	23	associate	associate	JJ
10_1101-436634	135	24	variants	variant	NNS
10_1101-436634	135	25	with	with	IN
10_1101-436634	135	26	specific	specific	JJ
10_1101-436634	135	27	cancer	cancer	NN
10_1101-436634	135	28	types	type	NNS
10_1101-436634	135	29	,	,	,
10_1101-436634	135	30	there	there	EX
10_1101-436634	135	31	has	have	VBZ
10_1101-436634	135	32	been	be	VBN
10_1101-436634	135	33	little	little	JJ
10_1101-436634	135	34	focus	focus	NN
10_1101-436634	135	35	on	on	IN
10_1101-436634	135	36	identifying	identify	VBG
10_1101-436634	135	37	such	such	JJ
10_1101-436634	135	38	associations	association	NNS
10_1101-436634	135	39	in	in	IN
10_1101-436634	135	40	splice	splice	NN
10_1101-436634	135	41	-	-	HYPH
10_1101-436634	135	42	altering	alter	VBG
10_1101-436634	135	43	variants	variant	NNS
10_1101-436634	135	44	,	,	,
10_1101-436634	135	45	even	even	RB
10_1101-436634	135	46	those	those	DT
10_1101-436634	135	47	in	in	IN
10_1101-436634	135	48	known	know	VBN
10_1101-436634	135	49	cancer	cancer	NN
10_1101-436634	135	50	genes	gene	NNS
10_1101-436634	135	51	.	.	.
10_1101-436634	136	1	TP53	tp53	NN
10_1101-436634	136	2	is	be	VBZ
10_1101-436634	136	3	a	a	DT
10_1101-436634	136	4	rare	rare	JJ
10_1101-436634	136	5	example	example	NN
10_1101-436634	136	6	whose	whose	WP$
10_1101-436634	136	7	splice	splice	NN
10_1101-436634	136	8	-	-	HYPH
10_1101-436634	136	9	altering	alter	VBG
10_1101-436634	136	10	variants	variant	NNS
10_1101-436634	136	11	are	be	VBP
10_1101-436634	136	12	well	well	RB
10_1101-436634	136	13	characterized	characterize	VBN
10_1101-436634	136	14	in	in	IN
10_1101-436634	136	15	numerous	numerous	JJ
10_1101-436634	136	16	cancer	cancer	NN
10_1101-436634	136	17	types33	types33	IN
10_1101-436634	136	18	.	.	.
10_1101-436634	137	1	As	as	IN
10_1101-436634	137	2	such	such	JJ
10_1101-436634	137	3	,	,	,
10_1101-436634	137	4	we	-PRON-	PRP
10_1101-436634	137	5	further	further	RB
10_1101-436634	137	6	analyzed	analyze	VBD
10_1101-436634	137	7	significant	significant	JJ
10_1101-436634	137	8	events	event	NNS
10_1101-436634	137	9	to	to	TO
10_1101-436634	137	10	identify	identify	VB
10_1101-436634	137	11	genes	gene	NNS
10_1101-436634	137	12	that	that	WDT
10_1101-436634	137	13	had	have	VBD
10_1101-436634	137	14	recurrent	recurrent	JJ
10_1101-436634	137	15	splice	splice	NN
10_1101-436634	137	16	altering	alter	VBG
10_1101-436634	137	17	variants	variant	NNS
10_1101-436634	137	18	.	.	.
10_1101-436634	138	1	Within	within	IN
10_1101-436634	138	2	each	each	DT
10_1101-436634	138	3	cohort	cohort	NN
10_1101-436634	138	4	,	,	,
10_1101-436634	138	5	we	-PRON-	PRP
10_1101-436634	138	6	looked	look	VBD
10_1101-436634	138	7	for	for	IN
10_1101-436634	138	8	recurrent	recurrent	JJ
10_1101-436634	138	9	genes	gene	NNS
10_1101-436634	138	10	using	use	VBG
10_1101-436634	138	11	two	two	CD
10_1101-436634	138	12	separate	separate	JJ
10_1101-436634	138	13	metrics	metric	NNS
10_1101-436634	138	14	:	:	:
10_1101-436634	138	15	a	a	DT
10_1101-436634	138	16	binomial	binomial	JJ
10_1101-436634	138	17	test	test	NN
10_1101-436634	138	18	p	p	NN
10_1101-436634	138	19	-	-	HYPH
10_1101-436634	138	20	value	value	NN
10_1101-436634	138	21	and	and	CC
10_1101-436634	138	22	the	the	DT
10_1101-436634	138	23	fraction	fraction	NN
10_1101-436634	138	24	of	of	IN
10_1101-436634	138	25	samples	sample	NNS
10_1101-436634	138	26	(	(	-LRB-
10_1101-436634	138	27	see	see	VB
10_1101-436634	138	28	Methods	method	NNS
10_1101-436634	138	29	)	)	-RRB-
10_1101-436634	138	30	.	.	.
10_1101-436634	139	1	For	for	IN
10_1101-436634	139	2	ranking	rank	VBG
10_1101-436634	139	3	and	and	CC
10_1101-436634	139	4	selecting	select	VBG
10_1101-436634	139	5	the	the	DT
10_1101-436634	139	6	most	most	RBS
10_1101-436634	139	7	recurrent	recurrent	JJ
10_1101-436634	139	8	genes	gene	NNS
10_1101-436634	139	9	,	,	,
10_1101-436634	139	10	each	each	DT
10_1101-436634	139	11	metric	metric	JJ
10_1101-436634	139	12	was	be	VBD
10_1101-436634	139	13	computed	compute	VBN
10_1101-436634	139	14	by	by	IN
10_1101-436634	139	15	pooling	pool	VBG
10_1101-436634	139	16	across	across	IN
10_1101-436634	139	17	all	all	DT
10_1101-436634	139	18	cohorts	cohort	NNS
10_1101-436634	139	19	.	.	.
10_1101-436634	140	1	For	for	IN
10_1101-436634	140	2	assessing	assess	VBG
10_1101-436634	140	3	cancer	cancer	NN
10_1101-436634	140	4	-	-	HYPH
10_1101-436634	140	5	type	type	NN
10_1101-436634	140	6	specificity	specificity	NN
10_1101-436634	140	7	,	,	,
10_1101-436634	140	8	each	each	DT
10_1101-436634	140	9	metric	metric	NN
10_1101-436634	140	10	was	be	VBD
10_1101-436634	140	11	then	then	RB
10_1101-436634	140	12	also	also	RB
10_1101-436634	140	13	computed	compute	VBN
10_1101-436634	140	14	using	use	VBG
10_1101-436634	140	15	only	only	RB
10_1101-436634	140	16	results	result	NNS
10_1101-436634	140	17	from	from	IN
10_1101-436634	140	18	a	a	DT
10_1101-436634	140	19	given	give	VBN
10_1101-436634	140	20	cancer	cancer	NN
10_1101-436634	140	21	cohort	cohort	NN
10_1101-436634	140	22	.	.	.
10_1101-436634	141	1	Since	since	IN
10_1101-436634	141	2	the	the	DT
10_1101-436634	141	3	mechanisms	mechanism	NNS
10_1101-436634	141	4	underlying	underlie	VBG
10_1101-436634	141	5	the	the	DT
10_1101-436634	141	6	creation	creation	NN
10_1101-436634	141	7	of	of	IN
10_1101-436634	141	8	novel	novel	JJ
10_1101-436634	141	9	junctions	junction	NNS
10_1101-436634	141	10	versus	versus	IN
10_1101-436634	141	11	the	the	DT
10_1101-436634	141	12	disruption	disruption	NN
10_1101-436634	141	13	of	of	IN
10_1101-436634	141	14	existing	exist	VBG
10_1101-436634	141	15	splicing	splicing	NN
10_1101-436634	141	16	patterns	pattern	NNS
10_1101-436634	141	17	may	may	MD
10_1101-436634	141	18	be	be	VB
10_1101-436634	141	19	different	different	JJ
10_1101-436634	141	20	,	,	,
10_1101-436634	141	21	analysis	analysis	NN
10_1101-436634	141	22	was	be	VBD
10_1101-436634	141	23	performed	perform	VBN
10_1101-436634	141	24	separately	separately	RB
10_1101-436634	141	25	for	for	IN
10_1101-436634	141	26	D	d	NN
10_1101-436634	141	27	/	/	SYM
10_1101-436634	141	28	A	A	NNP
10_1101-436634	141	29	/	/	SYM
10_1101-436634	141	30	NDA	NDA	NNP
10_1101-436634	141	31	junctions	junction	NNS
10_1101-436634	141	32	(	(	-LRB-
10_1101-436634	141	33	Figure	Figure	NNP
10_1101-436634	141	34	5	5	CD
10_1101-436634	141	35	,	,	,
10_1101-436634	141	36	Supplementary	Supplementary	NNP
10_1101-436634	141	37	Figure	Figure	NNP
10_1101-436634	141	38	6	6	CD
10_1101-436634	141	39	,	,	,
10_1101-436634	141	40	Supplementary	Supplementary	NNP
10_1101-436634	141	41	File	File	NNP
10_1101-436634	141	42	5	5	CD
10_1101-436634	141	43	)	)	-RRB-
10_1101-436634	141	44	and	and	CC
10_1101-436634	141	45	DA	DA	NNP
10_1101-436634	141	46	junctions	junction	NNS
10_1101-436634	141	47	(	(	-LRB-
10_1101-436634	141	48	Supplementary	Supplementary	NNP
10_1101-436634	141	49	Figure	Figure	NNP
10_1101-436634	141	50	7	7	CD
10_1101-436634	141	51	,	,	,
10_1101-436634	141	52	Supplementary	Supplementary	NNP
10_1101-436634	141	53	File	File	NNP
10_1101-436634	141	54	6	6	CD
10_1101-436634	141	55	)	)	-RRB-
10_1101-436634	141	56	,	,	,
10_1101-436634	141	57	which	which	WDT
10_1101-436634	141	58	allowed	allow	VBD
10_1101-436634	141	59	multiple	multiple	JJ
10_1101-436634	141	60	test	test	NN
10_1101-436634	141	61	correction	correction	NN
10_1101-436634	141	62	in	in	IN
10_1101-436634	141	63	accordance	accordance	NN
10_1101-436634	141	64	with	with	IN
10_1101-436634	141	65	the	the	DT
10_1101-436634	141	66	noise	noise	NN
10_1101-436634	141	67	of	of	IN
10_1101-436634	141	68	the	the	DT
10_1101-436634	141	69	respective	respective	JJ
10_1101-436634	141	70	data	datum	NNS
10_1101-436634	141	71	.	.	.
10_1101-436634	142	1	We	-PRON-	PRP
10_1101-436634	142	2	identified	identify	VBD
10_1101-436634	142	3	6,954	6,954	CD
10_1101-436634	142	4	genes	gene	NNS
10_1101-436634	142	5	in	in	IN
10_1101-436634	142	6	which	which	WDT
10_1101-436634	142	7	there	there	EX
10_1101-436634	142	8	was	be	VBD
10_1101-436634	142	9	least	least	RBS
10_1101-436634	142	10	one	one	CD
10_1101-436634	142	11	variant	variant	NN
10_1101-436634	142	12	predicted	predict	VBN
10_1101-436634	142	13	to	to	TO
10_1101-436634	142	14	influence	influence	VB
10_1101-436634	142	15	the	the	DT
10_1101-436634	142	16	splicing	splicing	NN
10_1101-436634	142	17	of	of	IN
10_1101-436634	142	18	a	a	DT
10_1101-436634	142	19	D	d	NN
10_1101-436634	142	20	/	/	SYM
10_1101-436634	142	21	A	A	NNP
10_1101-436634	142	22	/	/	SYM
10_1101-436634	142	23	NDA	NDA	NNP
10_1101-436634	142	24	junction	junction	NN
10_1101-436634	142	25	.	.	.
10_1101-436634	143	1	The	the	DT
10_1101-436634	143	2	99th	99th	JJ
10_1101-436634	143	3	percentile	percentile	NN
10_1101-436634	143	4	of	of	IN
10_1101-436634	143	5	these	these	DT
10_1101-436634	143	6	genes	gene	NNS
10_1101-436634	143	7	,	,	,
10_1101-436634	143	8	when	when	WRB
10_1101-436634	143	9	ranked	rank	VBN
10_1101-436634	143	10	by	by	IN
10_1101-436634	143	11	either	either	DT
10_1101-436634	143	12	metric	metric	NN
10_1101-436634	143	13	,	,	,
10_1101-436634	143	14	are	be	VBP
10_1101-436634	143	15	significantly	significantly	RB
10_1101-436634	143	16	enriched	enrich	VBN
10_1101-436634	143	17	for	for	IN
10_1101-436634	143	18	known	know	VBN
10_1101-436634	143	19	cancer	cancer	NN
10_1101-436634	143	20	genes	gene	NNS
10_1101-436634	143	21	,	,	,
10_1101-436634	143	22	as	as	IN
10_1101-436634	143	23	annotated	annotate	VBN
10_1101-436634	143	24	by	by	IN
10_1101-436634	143	25	the	the	DT
10_1101-436634	143	26	CGC	CGC	NNP
10_1101-436634	143	27	(	(	-LRB-
10_1101-436634	143	28	p=1.26E-19	p=1.26E-19	NNP
10_1101-436634	143	29	,	,	,
10_1101-436634	143	30	ranked	rank	VBN
10_1101-436634	143	31	by	by	IN
10_1101-436634	143	32	binomial	binomial	JJ
10_1101-436634	143	33	p	p	NN
10_1101-436634	143	34	-	-	HYPH
10_1101-436634	143	35	values	value	NNS
10_1101-436634	143	36	,	,	,
10_1101-436634	143	37	p=2.97E-24	p=2.97E-24	NNP
10_1101-436634	143	38	,	,	,
10_1101-436634	143	39	ranked	rank	VBN
10_1101-436634	143	40	by	by	IN
10_1101-436634	143	41	fraction	fraction	NN
10_1101-436634	143	42	of	of	IN
10_1101-436634	143	43	samples	sample	NNS
10_1101-436634	143	44	;	;	:
10_1101-436634	143	45	hypergeometric	hypergeometric	NN
10_1101-436634	143	46	test	test	NN
10_1101-436634	143	47	)	)	-RRB-
10_1101-436634	143	48	.	.	.
10_1101-436634	144	1	We	-PRON-	PRP
10_1101-436634	144	2	also	also	RB
10_1101-436634	144	3	identified	identify	VBD
10_1101-436634	144	4	3,643	3,643	CD
10_1101-436634	144	5	genes	gene	NNS
10_1101-436634	144	6	in	in	IN
10_1101-436634	144	7	which	which	WDT
10_1101-436634	144	8	there	there	EX
10_1101-436634	144	9	was	be	VBD
10_1101-436634	144	10	least	least	RBS
10_1101-436634	144	11	one	one	CD
10_1101-436634	144	12	variant	variant	NN
10_1101-436634	144	13	predicted	predict	VBN
10_1101-436634	144	14	to	to	TO
10_1101-436634	144	15	influence	influence	VB
10_1101-436634	144	16	the	the	DT
10_1101-436634	144	17	splicing	splicing	NN
10_1101-436634	144	18	of	of	IN
10_1101-436634	144	19	a	a	DT
10_1101-436634	144	20	DA	DA	NNP
10_1101-436634	144	21	(	(	-LRB-
10_1101-436634	144	22	known	know	VBN
10_1101-436634	144	23	)	)	-RRB-
10_1101-436634	144	24	junction	junction	NN
10_1101-436634	144	25	.	.	.
10_1101-436634	145	1	The	the	DT
10_1101-436634	145	2	99th	99th	JJ
10_1101-436634	145	3	percentile	percentile	NN
10_1101-436634	145	4	of	of	IN
10_1101-436634	145	5	these	these	DT
10_1101-436634	145	6	genes	gene	NNS
10_1101-436634	145	7	,	,	,
10_1101-436634	145	8	when	when	WRB
10_1101-436634	145	9	ranked	rank	VBN
10_1101-436634	145	10	by	by	IN
10_1101-436634	145	11	either	either	DT
10_1101-436634	145	12	metric	metric	NN
10_1101-436634	145	13	,	,	,
10_1101-436634	145	14	are	be	VBP
10_1101-436634	145	15	also	also	RB
10_1101-436634	145	16	significantly	significantly	RB
10_1101-436634	145	17	enriched	enrich	VBN
10_1101-436634	145	18	for	for	IN
10_1101-436634	145	19	known	know	VBN
10_1101-436634	145	20	cancer	cancer	NN
10_1101-436634	145	21	genes	gene	NNS
10_1101-436634	145	22	,	,	,
10_1101-436634	145	23	as	as	IN
10_1101-436634	145	24	annotated	annotate	VBN
10_1101-436634	145	25	by	by	IN
10_1101-436634	145	26	the	the	DT
10_1101-436634	145	27	Cancer	Cancer	NNP
10_1101-436634	145	28	Gene	Gene	NNP
10_1101-436634	145	29	Census	Census	NNP
10_1101-436634	145	30	(	(	-LRB-
10_1101-436634	145	31	p=1.00E-04	p=1.00E-04	NNP
10_1101-436634	145	32	,	,	,
10_1101-436634	145	33	ranked	rank	VBN
10_1101-436634	145	34	by	by	IN
10_1101-436634	145	35	binomial	binomial	JJ
10_1101-436634	145	36	p	p	NN
10_1101-436634	145	37	-	-	HYPH
10_1101-436634	145	38	values	value	NNS
10_1101-436634	145	39	,	,	,
10_1101-436634	145	40	p=3.56E-07	p=3.56E-07	NNP
10_1101-436634	145	41	,	,	,
10_1101-436634	145	42	ranked	rank	VBN
10_1101-436634	145	43	by	by	IN
10_1101-436634	145	44	fraction	fraction	NN
10_1101-436634	145	45	of	of	IN
10_1101-436634	145	46	samples	sample	NNS
10_1101-436634	145	47	;	;	:
10_1101-436634	145	48	hypergeometric	hypergeometric	NN
10_1101-436634	145	49	test	test	NN
10_1101-436634	145	50	)	)	-RRB-
10_1101-436634	145	51	.	.	.
10_1101-436634	146	1	We	-PRON-	PRP
10_1101-436634	146	2	also	also	RB
10_1101-436634	146	3	performed	perform	VBD
10_1101-436634	146	4	the	the	DT
10_1101-436634	146	5	same	same	JJ
10_1101-436634	146	6	analyses	analysis	NNS
10_1101-436634	146	7	using	use	VBG
10_1101-436634	146	8	either	either	CC
10_1101-436634	146	9	the	the	DT
10_1101-436634	146	10	TCGA	TCGA	NNP
10_1101-436634	146	11	or	or	CC
10_1101-436634	146	12	MGI	MGI	NNP
10_1101-436634	146	13	cohorts	cohort	NNS
10_1101-436634	146	14	alone	alone	RB
10_1101-436634	146	15	.	.	.
10_1101-436634	147	1	The	the	DT
10_1101-436634	147	2	TCGA	tcga	NN
10_1101-436634	147	3	-	-	HYPH
10_1101-436634	147	4	only	only	RB
10_1101-436634	147	5	analyses	analysis	NNS
10_1101-436634	147	6	gave	give	VBD
10_1101-436634	147	7	very	very	RB
10_1101-436634	147	8	similar	similar	JJ
10_1101-436634	147	9	results	result	NNS
10_1101-436634	147	10	to	to	IN
10_1101-436634	147	11	the	the	DT
10_1101-436634	147	12	combined	combine	VBN
10_1101-436634	147	13	analyses	analysis	NNS
10_1101-436634	147	14	,	,	,
10_1101-436634	147	15	with	with	IN
10_1101-436634	147	16	the	the	DT
10_1101-436634	147	17	99th	99th	JJ
10_1101-436634	147	18	percentile	percentile	NN
10_1101-436634	147	19	of	of	IN
10_1101-436634	147	20	genes	gene	NNS
10_1101-436634	147	21	found	find	VBN
10_1101-436634	147	22	in	in	IN
10_1101-436634	147	23	the	the	DT
10_1101-436634	147	24	D	d	NN
10_1101-436634	147	25	/	/	SYM
10_1101-436634	147	26	A	A	NNP
10_1101-436634	147	27	/	/	SYM
10_1101-436634	147	28	NDA	NDA	NNP
10_1101-436634	147	29	and	and	CC
10_1101-436634	147	30	DA	DA	NNP
10_1101-436634	147	31	analyses	analyse	VBZ
10_1101-436634	147	32	again	again	RB
10_1101-436634	147	33	being	be	VBG
10_1101-436634	147	34	enriched	enrich	VBN
10_1101-436634	147	35	for	for	IN
10_1101-436634	147	36	cancer	cancer	NN
10_1101-436634	147	37	genes	gene	NNS
10_1101-436634	147	38	(	(	-LRB-
10_1101-436634	147	39	Supplementary	Supplementary	NNP
10_1101-436634	147	40	Figures	Figures	NNPS
10_1101-436634	147	41	8	8	CD
10_1101-436634	147	42	and	and	CC
10_1101-436634	147	43	9	9	CD
10_1101-436634	147	44	;	;	:
10_1101-436634	147	45	Supplemental	Supplemental	NNP
10_1101-436634	147	46	Files	Files	NNP
10_1101-436634	147	47	5	5	CD
10_1101-436634	147	48	and	and	CC
10_1101-436634	147	49	6	6	CD
10_1101-436634	147	50	)	)	-RRB-
10_1101-436634	147	51	.	.	.
10_1101-436634	148	1	Due	due	IN
10_1101-436634	148	2	to	to	IN
10_1101-436634	148	3	small	small	JJ
10_1101-436634	148	4	cohort	cohort	NN
10_1101-436634	148	5	sizes	size	NNS
10_1101-436634	148	6	,	,	,
10_1101-436634	148	7	in	in	IN
10_1101-436634	148	8	the	the	DT
10_1101-436634	148	9	MGI	MGI	NNP
10_1101-436634	148	10	-	-	HYPH
10_1101-436634	148	11	only	only	RB
10_1101-436634	148	12	analyses	analysis	NNS
10_1101-436634	148	13	,	,	,
10_1101-436634	148	14	we	-PRON-	PRP
10_1101-436634	148	15	identified	identify	VBD
10_1101-436634	148	16	only	only	RB
10_1101-436634	148	17	329	329	CD
10_1101-436634	148	18	and	and	CC
10_1101-436634	148	19	208	208	CD
10_1101-436634	148	20	genes	gene	NNS
10_1101-436634	148	21	in	in	IN
10_1101-436634	148	22	the	the	DT
10_1101-436634	148	23	D	d	NN
10_1101-436634	148	24	/	/	SYM
10_1101-436634	148	25	A	A	NNP
10_1101-436634	148	26	/	/	SYM
10_1101-436634	148	27	NDA	NDA	NNP
10_1101-436634	148	28	and	and	CC
10_1101-436634	148	29	DA	DA	NNP
10_1101-436634	148	30	analyses	analysis	NNS
10_1101-436634	148	31	,	,	,
10_1101-436634	148	32	respectively	respectively	RB
10_1101-436634	148	33	.	.	.
10_1101-436634	149	1	The	the	DT
10_1101-436634	149	2	99th	99th	JJ
10_1101-436634	149	3	percentile	percentile	NN
10_1101-436634	149	4	of	of	IN
10_1101-436634	149	5	genes	gene	NNS
10_1101-436634	149	6	from	from	IN
10_1101-436634	149	7	these	these	DT
10_1101-436634	149	8	analyses	analysis	NNS
10_1101-436634	149	9	,	,	,
10_1101-436634	149	10	respectively	respectively	RB
10_1101-436634	149	11	,	,	,
10_1101-436634	149	12	were	be	VBD
10_1101-436634	149	13	not	not	RB
10_1101-436634	149	14	significantly	significantly	RB
10_1101-436634	149	15	enriched	enrich	VBN
10_1101-436634	149	16	for	for	IN
10_1101-436634	149	17	cancer	cancer	NN
10_1101-436634	149	18	genes	gene	NNS
10_1101-436634	149	19	(	(	-LRB-
10_1101-436634	149	20	Supplementary	Supplementary	NNP
10_1101-436634	149	21	Figures	Figures	NNPS
10_1101-436634	149	22	10	10	CD
10_1101-436634	149	23	and	and	CC
10_1101-436634	149	24	11	11	CD
10_1101-436634	149	25	;	;	:
10_1101-436634	149	26	Supplemental	Supplemental	NNP
10_1101-436634	149	27	Files	Files	NNP
10_1101-436634	149	28	5	5	CD
10_1101-436634	149	29	and	and	CC
10_1101-436634	149	30	6	6	CD
10_1101-436634	149	31	)	)	-RRB-
10_1101-436634	149	32	.	.	.
10_1101-436634	150	1	When	when	WRB
10_1101-436634	150	2	analyzing	analyze	VBG
10_1101-436634	150	3	D	d	NN
10_1101-436634	150	4	,	,	,
10_1101-436634	150	5	A	a	NN
10_1101-436634	150	6	,	,	,
10_1101-436634	150	7	and	and	CC
10_1101-436634	150	8	NDA	NDA	NNP
10_1101-436634	150	9	junctions	junction	NNS
10_1101-436634	150	10	,	,	,
10_1101-436634	150	11	we	-PRON-	PRP
10_1101-436634	150	12	saw	see	VBD
10_1101-436634	150	13	an	an	DT
10_1101-436634	150	14	enrichment	enrichment	NN
10_1101-436634	150	15	for	for	IN
10_1101-436634	150	16	known	know	VBN
10_1101-436634	150	17	tumor	tumor	NN
10_1101-436634	150	18	suppressor	suppressor	NN
10_1101-436634	150	19	genes	gene	NNS
10_1101-436634	150	20	among	among	IN
10_1101-436634	150	21	the	the	DT
10_1101-436634	150	22	most	most	JJS
10_1101-436634	150	23	splice	splice	NN
10_1101-436634	150	24	disrupted	disrupt	VBN
10_1101-436634	150	25	genes	gene	NNS
10_1101-436634	150	26	,	,	,
10_1101-436634	150	27	including	include	VBG
10_1101-436634	150	28	several	several	JJ
10_1101-436634	150	29	examples	example	NNS
10_1101-436634	150	30	where	where	WRB
10_1101-436634	150	31	splice	splice	NN
10_1101-436634	150	32	.CC	.CC	,
10_1101-436634	150	33	-	-	HYPH
10_1101-436634	150	34	BY	by	IN
10_1101-436634	150	35	-	-	HYPH
10_1101-436634	150	36	NC	NC	NNP
10_1101-436634	150	37	-	-	HYPH
10_1101-436634	150	38	ND	ND	NNP
10_1101-436634	150	39	4.0	4.0	CD
10_1101-436634	150	40	International	international	JJ
10_1101-436634	150	41	licensea	licensea	NNS
10_1101-436634	150	42	certified	certify	VBN
10_1101-436634	150	43	by	by	IN
10_1101-436634	150	44	peer	peer	NN
10_1101-436634	150	45	review	review	NN
10_1101-436634	150	46	)	)	-RRB-
10_1101-436634	150	47	is	be	VBZ
10_1101-436634	150	48	the	the	DT
10_1101-436634	150	49	author	author	NN
10_1101-436634	150	50	/	/	SYM
10_1101-436634	150	51	funder	funder	NN
10_1101-436634	150	52	,	,	,
10_1101-436634	150	53	who	who	WP
10_1101-436634	150	54	has	have	VBZ
10_1101-436634	150	55	granted	grant	VBN
10_1101-436634	150	56	bioRxiv	biorxiv	IN
10_1101-436634	150	57	a	a	DT
10_1101-436634	150	58	license	license	NN
10_1101-436634	150	59	to	to	TO
10_1101-436634	150	60	display	display	VB
10_1101-436634	150	61	the	the	DT
10_1101-436634	150	62	preprint	preprint	NN
10_1101-436634	150	63	in	in	IN
10_1101-436634	150	64	perpetuity	perpetuity	NN
10_1101-436634	150	65	.	.	.
10_1101-436634	151	1	It	-PRON-	PRP
10_1101-436634	151	2	is	be	VBZ
10_1101-436634	151	3	made	make	VBN
10_1101-436634	151	4	available	available	JJ
10_1101-436634	151	5	under	under	IN
10_1101-436634	151	6	The	the	DT
10_1101-436634	151	7	copyright	copyright	NN
10_1101-436634	151	8	holder	holder	NN
10_1101-436634	151	9	for	for	IN
10_1101-436634	151	10	this	this	DT
10_1101-436634	151	11	preprint	preprint	NN
10_1101-436634	151	12	(	(	-LRB-
10_1101-436634	151	13	which	which	WDT
10_1101-436634	151	14	was	be	VBD
10_1101-436634	151	15	notthis	notthis	DT
10_1101-436634	151	16	version	version	NN
10_1101-436634	151	17	posted	post	VBN
10_1101-436634	151	18	January	January	NNP
10_1101-436634	151	19	5	5	CD
10_1101-436634	151	20	,	,	,
10_1101-436634	151	21	2021	2021	CD
10_1101-436634	151	22	.	.	.
10_1101-436634	151	23	;	;	:
10_1101-436634	151	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	151	25	:	:	:
10_1101-436634	151	26	bioRxiv	biorxiv	VB
10_1101-436634	151	27	preprint	preprint	NN
10_1101-436634	151	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	151	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	151	30	8	8	CD
10_1101-436634	151	31	disruption	disruption	NN
10_1101-436634	151	32	is	be	VBZ
10_1101-436634	151	33	a	a	DT
10_1101-436634	151	34	known	know	VBN
10_1101-436634	151	35	mechanism	mechanism	NN
10_1101-436634	151	36	such	such	JJ
10_1101-436634	151	37	as	as	IN
10_1101-436634	151	38	TP53	TP53	NNP
10_1101-436634	151	39	,	,	,
10_1101-436634	151	40	PTEN	PTEN	NNP
10_1101-436634	151	41	,	,	,
10_1101-436634	151	42	CDKN2A	CDKN2A	NNP
10_1101-436634	151	43	,	,	,
10_1101-436634	151	44	and	and	CC
10_1101-436634	151	45	RB1	RB1	NNP
10_1101-436634	151	46	.	.	.
10_1101-436634	152	1	Specifically	specifically	RB
10_1101-436634	152	2	,	,	,
10_1101-436634	152	3	in	in	IN
10_1101-436634	152	4	the	the	DT
10_1101-436634	152	5	case	case	NN
10_1101-436634	152	6	of	of	IN
10_1101-436634	152	7	TP53	TP53	NNP
10_1101-436634	152	8	,	,	,
10_1101-436634	152	9	we	-PRON-	PRP
10_1101-436634	152	10	identified	identify	VBD
10_1101-436634	152	11	428	428	CD
10_1101-436634	152	12	variants	variant	NNS
10_1101-436634	152	13	that	that	WDT
10_1101-436634	152	14	were	be	VBD
10_1101-436634	152	15	significantly	significantly	RB
10_1101-436634	152	16	associated	associate	VBN
10_1101-436634	152	17	with	with	IN
10_1101-436634	152	18	at	at	RB
10_1101-436634	152	19	least	least	RBS
10_1101-436634	152	20	one	one	CD
10_1101-436634	152	21	novel	novel	NN
10_1101-436634	152	22	splicing	splicing	NN
10_1101-436634	152	23	event	event	NN
10_1101-436634	152	24	.	.	.
10_1101-436634	153	1	One	one	CD
10_1101-436634	153	2	such	such	JJ
10_1101-436634	153	3	example	example	NN
10_1101-436634	153	4	is	be	VBZ
10_1101-436634	153	5	the	the	DT
10_1101-436634	153	6	intronic	intronic	JJ
10_1101-436634	153	7	SNV	SNV	NNP
10_1101-436634	153	8	(	(	-LRB-
10_1101-436634	153	9	GRCh38	GRCh38	NNP
10_1101-436634	153	10	,	,	,
10_1101-436634	153	11	chr17	chr17	NN
10_1101-436634	153	12	:	:	:
10_1101-436634	153	13	g.7673609C	g.7673609c	XX
10_1101-436634	153	14	>	>	XX
10_1101-436634	153	15	A	a	NN
10_1101-436634	153	16	)	)	-RRB-
10_1101-436634	153	17	that	that	WDT
10_1101-436634	153	18	was	be	VBD
10_1101-436634	153	19	identified	identify	VBN
10_1101-436634	153	20	in	in	IN
10_1101-436634	153	21	an	an	DT
10_1101-436634	153	22	OSCC	OSCC	NNP
10_1101-436634	153	23	sample	sample	NN
10_1101-436634	153	24	and	and	CC
10_1101-436634	153	25	was	be	VBD
10_1101-436634	153	26	associated	associate	VBN
10_1101-436634	153	27	with	with	IN
10_1101-436634	153	28	an	an	DT
10_1101-436634	153	29	exon	exon	JJ
10_1101-436634	153	30	skipping	skipping	NN
10_1101-436634	153	31	event	event	NN
10_1101-436634	153	32	and	and	CC
10_1101-436634	153	33	an	an	DT
10_1101-436634	153	34	alternate	alternate	JJ
10_1101-436634	153	35	acceptor	acceptor	NN
10_1101-436634	153	36	site	site	NN
10_1101-436634	153	37	usage	usage	NN
10_1101-436634	153	38	event	event	NN
10_1101-436634	153	39	,	,	,
10_1101-436634	153	40	with	with	IN
10_1101-436634	153	41	23	23	CD
10_1101-436634	153	42	and	and	CC
10_1101-436634	153	43	41	41	CD
10_1101-436634	153	44	reads	read	NNS
10_1101-436634	153	45	of	of	IN
10_1101-436634	153	46	support	support	NN
10_1101-436634	153	47	,	,	,
10_1101-436634	153	48	respectively	respectively	RB
10_1101-436634	153	49	(	(	-LRB-
10_1101-436634	153	50	Supplemental	Supplemental	NNP
10_1101-436634	153	51	Figure	Figure	NNP
10_1101-436634	153	52	12	12	CD
10_1101-436634	153	53	)	)	-RRB-
10_1101-436634	153	54	.	.	.
10_1101-436634	154	1	The	the	DT
10_1101-436634	154	2	cancer	cancer	NN
10_1101-436634	154	3	types	type	NNS
10_1101-436634	154	4	in	in	IN
10_1101-436634	154	5	which	which	WDT
10_1101-436634	154	6	we	-PRON-	PRP
10_1101-436634	154	7	find	find	VBP
10_1101-436634	154	8	splice	splice	NN
10_1101-436634	154	9	disruption	disruption	NN
10_1101-436634	154	10	of	of	IN
10_1101-436634	154	11	TP53	TP53	NNP
10_1101-436634	154	12	and	and	CC
10_1101-436634	154	13	other	other	JJ
10_1101-436634	154	14	known	know	VBN
10_1101-436634	154	15	cancer	cancer	NN
10_1101-436634	154	16	genes	gene	NNS
10_1101-436634	154	17	is	be	VBZ
10_1101-436634	154	18	in	in	IN
10_1101-436634	154	19	concordance	concordance	NN
10_1101-436634	154	20	with	with	IN
10_1101-436634	154	21	associations	association	NNS
10_1101-436634	154	22	between	between	IN
10_1101-436634	154	23	genes	gene	NNS
10_1101-436634	154	24	and	and	CC
10_1101-436634	154	25	cancer	cancer	NN
10_1101-436634	154	26	types	type	NNS
10_1101-436634	154	27	described	describe	VBN
10_1101-436634	154	28	by	by	IN
10_1101-436634	154	29	CGC	CGC	NNP
10_1101-436634	154	30	and	and	CC
10_1101-436634	154	31	CHASMplus27,34	CHASMplus27,34	NNP
10_1101-436634	154	32	.	.	.
10_1101-436634	155	1	Our	-PRON-	PRP$
10_1101-436634	155	2	analysis	analysis	NN
10_1101-436634	155	3	’s	’s	POS
10_1101-436634	155	4	recovery	recovery	NN
10_1101-436634	155	5	of	of	IN
10_1101-436634	155	6	known	know	VBN
10_1101-436634	155	7	drivers	driver	NNS
10_1101-436634	155	8	,	,	,
10_1101-436634	155	9	many	many	JJ
10_1101-436634	155	10	of	of	IN
10_1101-436634	155	11	which	which	WDT
10_1101-436634	155	12	with	with	IN
10_1101-436634	155	13	known	know	VBN
10_1101-436634	155	14	susceptibilities	susceptibility	NNS
10_1101-436634	155	15	to	to	IN
10_1101-436634	155	16	splicing	splice	VBG
10_1101-436634	155	17	dysregulation	dysregulation	NN
10_1101-436634	155	18	in	in	IN
10_1101-436634	155	19	cancer	cancer	NN
10_1101-436634	155	20	,	,	,
10_1101-436634	155	21	indicates	indicate	VBZ
10_1101-436634	155	22	the	the	DT
10_1101-436634	155	23	ability	ability	NN
10_1101-436634	155	24	of	of	IN
10_1101-436634	155	25	our	-PRON-	PRP$
10_1101-436634	155	26	method	method	NN
10_1101-436634	155	27	to	to	TO
10_1101-436634	155	28	identify	identify	VB
10_1101-436634	155	29	true	true	JJ
10_1101-436634	155	30	splicing	splicing	NN
10_1101-436634	155	31	effects	effect	NNS
10_1101-436634	155	32	that	that	WDT
10_1101-436634	155	33	are	be	VBP
10_1101-436634	155	34	likely	likely	RB
10_1101-436634	155	35	cancer	cancer	NN
10_1101-436634	155	36	-	-	HYPH
10_1101-436634	155	37	relevant	relevant	JJ
10_1101-436634	155	38	.	.	.
10_1101-436634	156	1	Another	another	DT
10_1101-436634	156	2	cancer	cancer	NN
10_1101-436634	156	3	gene	gene	NN
10_1101-436634	156	4	that	that	WDT
10_1101-436634	156	5	we	-PRON-	PRP
10_1101-436634	156	6	found	find	VBD
10_1101-436634	156	7	to	to	TO
10_1101-436634	156	8	have	have	VB
10_1101-436634	156	9	a	a	DT
10_1101-436634	156	10	recurrence	recurrence	NN
10_1101-436634	156	11	of	of	IN
10_1101-436634	156	12	splicing	splice	VBG
10_1101-436634	156	13	altering	alter	VBG
10_1101-436634	156	14	variants	variant	NNS
10_1101-436634	156	15	was	be	VBD
10_1101-436634	156	16	B2M.	B2M.	NNP
10_1101-436634	157	1	Specifically	specifically	RB
10_1101-436634	157	2	,	,	,
10_1101-436634	157	3	we	-PRON-	PRP
10_1101-436634	157	4	identified	identify	VBD
10_1101-436634	157	5	six	six	CD
10_1101-436634	157	6	samples	sample	NNS
10_1101-436634	157	7	with	with	IN
10_1101-436634	157	8	intronic	intronic	JJ
10_1101-436634	157	9	variants	variant	NNS
10_1101-436634	157	10	on	on	IN
10_1101-436634	157	11	either	either	DT
10_1101-436634	157	12	side	side	NN
10_1101-436634	157	13	of	of	IN
10_1101-436634	157	14	exon	exon	JJ
10_1101-436634	157	15	2	2	CD
10_1101-436634	157	16	(	(	-LRB-
10_1101-436634	157	17	Figure	Figure	NNP
10_1101-436634	157	18	6	6	CD
10_1101-436634	157	19	)	)	-RRB-
10_1101-436634	157	20	.	.	.
10_1101-436634	158	1	While	while	IN
10_1101-436634	158	2	mutations	mutation	NNS
10_1101-436634	158	3	have	have	VBP
10_1101-436634	158	4	been	be	VBN
10_1101-436634	158	5	identified	identify	VBN
10_1101-436634	158	6	and	and	CC
10_1101-436634	158	7	studied	study	VBN
10_1101-436634	158	8	within	within	IN
10_1101-436634	158	9	exon	exon	NNP
10_1101-436634	158	10	2	2	CD
10_1101-436634	158	11	,	,	,
10_1101-436634	158	12	we	-PRON-	PRP
10_1101-436634	158	13	did	do	VBD
10_1101-436634	158	14	not	not	RB
10_1101-436634	158	15	find	find	VB
10_1101-436634	158	16	literature	literature	NN
10_1101-436634	158	17	that	that	WDT
10_1101-436634	158	18	specifically	specifically	RB
10_1101-436634	158	19	identified	identify	VBN
10_1101-436634	158	20	intronic	intronic	JJ
10_1101-436634	158	21	variants	variant	NNS
10_1101-436634	158	22	near	near	IN
10_1101-436634	158	23	exon	exon	NNP
10_1101-436634	158	24	2	2	CD
10_1101-436634	158	25	as	as	IN
10_1101-436634	158	26	a	a	DT
10_1101-436634	158	27	mechanism	mechanism	NN
10_1101-436634	158	28	for	for	IN
10_1101-436634	158	29	disrupting	disrupt	VBG
10_1101-436634	158	30	B2M35	b2m35	NN
10_1101-436634	158	31	.	.	.
10_1101-436634	159	1	These	these	DT
10_1101-436634	159	2	mutations	mutation	NNS
10_1101-436634	159	3	were	be	VBD
10_1101-436634	159	4	identified	identify	VBN
10_1101-436634	159	5	by	by	IN
10_1101-436634	159	6	VEP	VEP	NNP
10_1101-436634	159	7	to	to	TO
10_1101-436634	159	8	be	be	VB
10_1101-436634	159	9	either	either	CC
10_1101-436634	159	10	splice	splice	NN
10_1101-436634	159	11	acceptor	acceptor	NN
10_1101-436634	159	12	variant	variant	NN
10_1101-436634	159	13	or	or	CC
10_1101-436634	159	14	a	a	DT
10_1101-436634	159	15	splice	splice	NN
10_1101-436634	159	16	donor	donor	NN
10_1101-436634	159	17	variant	variant	JJ
10_1101-436634	159	18	and	and	CC
10_1101-436634	159	19	were	be	VBD
10_1101-436634	159	20	also	also	RB
10_1101-436634	159	21	identified	identify	VBN
10_1101-436634	159	22	by	by	IN
10_1101-436634	159	23	Veridical	Veridical	NNP
10_1101-436634	159	24	.	.	.
10_1101-436634	160	1	MiSplice	MiSplice	NNP
10_1101-436634	160	2	was	be	VBD
10_1101-436634	160	3	able	able	JJ
10_1101-436634	160	4	to	to	TO
10_1101-436634	160	5	predict	predict	VB
10_1101-436634	160	6	one	one	CD
10_1101-436634	160	7	of	of	IN
10_1101-436634	160	8	the	the	DT
10_1101-436634	160	9	novel	novel	JJ
10_1101-436634	160	10	junctions	junction	NNS
10_1101-436634	160	11	for	for	IN
10_1101-436634	160	12	each	each	DT
10_1101-436634	160	13	variant	variant	JJ
10_1101-436634	160	14	but	but	CC
10_1101-436634	160	15	failed	fail	VBD
10_1101-436634	160	16	to	to	TO
10_1101-436634	160	17	predict	predict	VB
10_1101-436634	160	18	additional	additional	JJ
10_1101-436634	160	19	novel	novel	JJ
10_1101-436634	160	20	junctions	junction	NNS
10_1101-436634	160	21	due	due	JJ
10_1101-436634	160	22	to	to	IN
10_1101-436634	160	23	the	the	DT
10_1101-436634	160	24	limitation	limitation	NN
10_1101-436634	160	25	of	of	IN
10_1101-436634	160	26	that	that	DT
10_1101-436634	160	27	tool	tool	NN
10_1101-436634	160	28	to	to	TO
10_1101-436634	160	29	only	only	RB
10_1101-436634	160	30	predict	predict	VB
10_1101-436634	160	31	one	one	CD
10_1101-436634	160	32	novel	novel	JJ
10_1101-436634	160	33	acceptor	acceptor	NN
10_1101-436634	160	34	and	and	CC
10_1101-436634	160	35	donor	donor	NN
10_1101-436634	160	36	site	site	NN
10_1101-436634	160	37	per	per	IN
10_1101-436634	160	38	variant	variant	NN
10_1101-436634	160	39	.	.	.
10_1101-436634	161	1	Notably	notably	RB
10_1101-436634	161	2	,	,	,
10_1101-436634	161	3	4	4	CD
10_1101-436634	161	4	out	out	IN
10_1101-436634	161	5	of	of	IN
10_1101-436634	161	6	the	the	DT
10_1101-436634	161	7	6	6	CD
10_1101-436634	161	8	samples	sample	NNS
10_1101-436634	161	9	that	that	WDT
10_1101-436634	161	10	these	these	DT
10_1101-436634	161	11	variants	variant	NNS
10_1101-436634	161	12	were	be	VBD
10_1101-436634	161	13	found	find	VBN
10_1101-436634	161	14	in	in	IN
10_1101-436634	161	15	are	be	VBP
10_1101-436634	161	16	MSI	MSI	NNP
10_1101-436634	161	17	-	-	HYPH
10_1101-436634	161	18	H	H	NNP
10_1101-436634	161	19	(	(	-LRB-
10_1101-436634	161	20	Microsatellite	Microsatellite	NNP
10_1101-436634	161	21	instability	instability	NN
10_1101-436634	161	22	-	-	HYPH
10_1101-436634	161	23	high	high	NN
10_1101-436634	161	24	)	)	-RRB-
10_1101-436634	161	25	tumors36	tumors36	NN
10_1101-436634	161	26	.	.	.
10_1101-436634	162	1	Mutations	mutation	NNS
10_1101-436634	162	2	in	in	IN
10_1101-436634	162	3	B2	B2	NNP
10_1101-436634	162	4	M	M	NNP
10_1101-436634	162	5	,	,	,
10_1101-436634	162	6	particularly	particularly	RB
10_1101-436634	162	7	within	within	IN
10_1101-436634	162	8	colorectal	colorectal	JJ
10_1101-436634	162	9	MSI	MSI	NNP
10_1101-436634	162	10	-	-	HYPH
10_1101-436634	162	11	H	h	NN
10_1101-436634	162	12	tumors	tumor	NNS
10_1101-436634	162	13	,	,	,
10_1101-436634	162	14	have	have	VBP
10_1101-436634	162	15	been	be	VBN
10_1101-436634	162	16	identified	identify	VBN
10_1101-436634	162	17	as	as	IN
10_1101-436634	162	18	a	a	DT
10_1101-436634	162	19	method	method	NN
10_1101-436634	162	20	for	for	IN
10_1101-436634	162	21	tumors	tumor	NNS
10_1101-436634	162	22	to	to	TO
10_1101-436634	162	23	become	become	VB
10_1101-436634	162	24	incapable	incapable	JJ
10_1101-436634	162	25	of	of	IN
10_1101-436634	162	26	HLA	HLA	NNP
10_1101-436634	162	27	class	class	NN
10_1101-436634	162	28	I	-PRON-	PRP
10_1101-436634	162	29	antigen	antigen	NN
10_1101-436634	162	30	-	-	HYPH
10_1101-436634	162	31	mediated	mediate	VBN
10_1101-436634	162	32	presentation37	presentation37	NNS
10_1101-436634	162	33	.	.	.
10_1101-436634	163	1	Furthermore	furthermore	RB
10_1101-436634	163	2	,	,	,
10_1101-436634	163	3	in	in	IN
10_1101-436634	163	4	a	a	DT
10_1101-436634	163	5	study	study	NN
10_1101-436634	163	6	of	of	IN
10_1101-436634	163	7	patients	patient	NNS
10_1101-436634	163	8	treated	treat	VBN
10_1101-436634	163	9	with	with	IN
10_1101-436634	163	10	immune	immune	JJ
10_1101-436634	163	11	checkpoint	checkpoint	NN
10_1101-436634	163	12	blockade	blockade	NN
10_1101-436634	163	13	(	(	-LRB-
10_1101-436634	163	14	ICB	ICB	NNP
10_1101-436634	163	15	)	)	-RRB-
10_1101-436634	163	16	therapy	therapy	NN
10_1101-436634	163	17	,	,	,
10_1101-436634	163	18	defects	defect	NNS
10_1101-436634	163	19	to	to	IN
10_1101-436634	163	20	B2	B2	NNP
10_1101-436634	163	21	M	M	NNP
10_1101-436634	163	22	were	be	VBD
10_1101-436634	163	23	observed	observe	VBN
10_1101-436634	163	24	in	in	IN
10_1101-436634	163	25	29.4	29.4	CD
10_1101-436634	163	26	%	%	NN
10_1101-436634	163	27	of	of	IN
10_1101-436634	163	28	patients	patient	NNS
10_1101-436634	163	29	with	with	IN
10_1101-436634	163	30	progressing	progress	VBG
10_1101-436634	163	31	disease38	disease38	NNP
10_1101-436634	163	32	.	.	.
10_1101-436634	164	1	In	in	IN
10_1101-436634	164	2	the	the	DT
10_1101-436634	164	3	same	same	JJ
10_1101-436634	164	4	study	study	NN
10_1101-436634	164	5	,	,	,
10_1101-436634	164	6	B2	B2	NNP
10_1101-436634	164	7	M	M	NNP
10_1101-436634	164	8	mutations	mutation	NNS
10_1101-436634	164	9	were	be	VBD
10_1101-436634	164	10	exclusively	exclusively	RB
10_1101-436634	164	11	seen	see	VBN
10_1101-436634	164	12	in	in	IN
10_1101-436634	164	13	pretreatment	pretreatment	JJ
10_1101-436634	164	14	samples	sample	NNS
10_1101-436634	164	15	from	from	IN
10_1101-436634	164	16	patients	patient	NNS
10_1101-436634	164	17	who	who	WP
10_1101-436634	164	18	did	do	VBD
10_1101-436634	164	19	not	not	RB
10_1101-436634	164	20	respond	respond	VB
10_1101-436634	164	21	to	to	IN
10_1101-436634	164	22	ICB	ICB	NNP
10_1101-436634	164	23	or	or	CC
10_1101-436634	164	24	in	in	IN
10_1101-436634	164	25	post-	post-	NNP
10_1101-436634	164	26	progression	progression	NN
10_1101-436634	164	27	samples	sample	NNS
10_1101-436634	164	28	after	after	IN
10_1101-436634	164	29	initial	initial	JJ
10_1101-436634	164	30	response	response	NN
10_1101-436634	164	31	to	to	IN
10_1101-436634	164	32	ICB38	ICB38	NNP
10_1101-436634	164	33	.	.	.
10_1101-436634	165	1	There	there	EX
10_1101-436634	165	2	are	be	VBP
10_1101-436634	165	3	several	several	JJ
10_1101-436634	165	4	genes	gene	NNS
10_1101-436634	165	5	that	that	WDT
10_1101-436634	165	6	are	be	VBP
10_1101-436634	165	7	responsible	responsible	JJ
10_1101-436634	165	8	for	for	IN
10_1101-436634	165	9	the	the	DT
10_1101-436634	165	10	processing	processing	NN
10_1101-436634	165	11	,	,	,
10_1101-436634	165	12	loading	loading	NN
10_1101-436634	165	13	,	,	,
10_1101-436634	165	14	and	and	CC
10_1101-436634	165	15	presentation	presentation	NN
10_1101-436634	165	16	of	of	IN
10_1101-436634	165	17	antigens	antigen	NNS
10_1101-436634	165	18	,	,	,
10_1101-436634	165	19	and	and	CC
10_1101-436634	165	20	have	have	VBP
10_1101-436634	165	21	been	be	VBN
10_1101-436634	165	22	shown	show	VBN
10_1101-436634	165	23	to	to	TO
10_1101-436634	165	24	be	be	VB
10_1101-436634	165	25	mutated	mutate	VBN
10_1101-436634	165	26	in	in	IN
10_1101-436634	165	27	cancers39	cancers39	NNP
10_1101-436634	165	28	.	.	.
10_1101-436634	166	1	However	however	RB
10_1101-436634	166	2	,	,	,
10_1101-436634	166	3	no	no	DT
10_1101-436634	166	4	proteins	protein	NNS
10_1101-436634	166	5	can	can	MD
10_1101-436634	166	6	be	be	VB
10_1101-436634	166	7	substituted	substitute	VBN
10_1101-436634	166	8	for	for	IN
10_1101-436634	166	9	B2	B2	NNP
10_1101-436634	166	10	M	M	NNP
10_1101-436634	166	11	in	in	IN
10_1101-436634	166	12	HLA	HLA	NNP
10_1101-436634	166	13	class	class	NN
10_1101-436634	166	14	I	-PRON-	PRP
10_1101-436634	166	15	presentation	presentation	NN
10_1101-436634	166	16	,	,	,
10_1101-436634	166	17	thus	thus	RB
10_1101-436634	166	18	making	make	VBG
10_1101-436634	166	19	the	the	DT
10_1101-436634	166	20	loss	loss	NN
10_1101-436634	166	21	of	of	IN
10_1101-436634	166	22	B2	b2	NN
10_1101-436634	166	23	M	M	NNP
10_1101-436634	166	24	a	a	DT
10_1101-436634	166	25	particularly	particularly	RB
10_1101-436634	166	26	robust	robust	JJ
10_1101-436634	166	27	method	method	NN
10_1101-436634	166	28	for	for	IN
10_1101-436634	166	29	ICB	ICB	NNP
10_1101-436634	166	30	resistance40	resistance40	NNP
10_1101-436634	166	31	.	.	.
10_1101-436634	167	1	We	-PRON-	PRP
10_1101-436634	167	2	also	also	RB
10_1101-436634	167	3	observe	observe	VBP
10_1101-436634	167	4	exonic	exonic	JJ
10_1101-436634	167	5	variants	variant	NNS
10_1101-436634	167	6	and	and	CC
10_1101-436634	167	7	variants	variant	NNS
10_1101-436634	167	8	further	far	RBR
10_1101-436634	167	9	in	in	IN
10_1101-436634	167	10	intronic	intronic	JJ
10_1101-436634	167	11	regions	region	NNS
10_1101-436634	167	12	that	that	WDT
10_1101-436634	167	13	disrupt	disrupt	VBP
10_1101-436634	167	14	canonical	canonical	JJ
10_1101-436634	167	15	splicing	splicing	NN
10_1101-436634	167	16	of	of	IN
10_1101-436634	167	17	B2M.	B2M.	NNP
10_1101-436634	168	1	These	these	DT
10_1101-436634	168	2	findings	finding	NNS
10_1101-436634	168	3	indicate	indicate	VBP
10_1101-436634	168	4	that	that	IN
10_1101-436634	168	5	intronic	intronic	JJ
10_1101-436634	168	6	variants	variant	NNS
10_1101-436634	168	7	that	that	WDT
10_1101-436634	168	8	result	result	VBP
10_1101-436634	168	9	in	in	IN
10_1101-436634	168	10	alternative	alternative	JJ
10_1101-436634	168	11	splice	splice	NN
10_1101-436634	168	12	products	product	NNS
10_1101-436634	168	13	within	within	IN
10_1101-436634	168	14	B2	b2	NN
10_1101-436634	168	15	M	M	NNP
10_1101-436634	168	16	may	may	MD
10_1101-436634	168	17	be	be	VB
10_1101-436634	168	18	a	a	DT
10_1101-436634	168	19	mechanism	mechanism	NN
10_1101-436634	168	20	for	for	IN
10_1101-436634	168	21	immune	immune	JJ
10_1101-436634	168	22	escape	escape	NN
10_1101-436634	168	23	within	within	IN
10_1101-436634	168	24	tumor	tumor	NN
10_1101-436634	168	25	samples	sample	NNS
10_1101-436634	168	26	.	.	.
10_1101-436634	169	1	We	-PRON-	PRP
10_1101-436634	169	2	also	also	RB
10_1101-436634	169	3	identify	identify	VBP
10_1101-436634	169	4	recurrent	recurrent	JJ
10_1101-436634	169	5	splice	splice	NN
10_1101-436634	169	6	altering	alter	VBG
10_1101-436634	169	7	variants	variant	NNS
10_1101-436634	169	8	in	in	IN
10_1101-436634	169	9	genes	gene	NNS
10_1101-436634	169	10	not	not	RB
10_1101-436634	169	11	known	know	VBN
10_1101-436634	169	12	to	to	TO
10_1101-436634	169	13	be	be	VB
10_1101-436634	169	14	cancer	cancer	NN
10_1101-436634	169	15	genes	gene	NNS
10_1101-436634	169	16	(	(	-LRB-
10_1101-436634	169	17	according	accord	VBG
10_1101-436634	169	18	to	to	IN
10_1101-436634	169	19	CGC	CGC	NNP
10_1101-436634	169	20	)	)	-RRB-
10_1101-436634	169	21	,	,	,
10_1101-436634	169	22	such	such	JJ
10_1101-436634	169	23	as	as	IN
10_1101-436634	169	24	RNF145	RNF145	NNP
10_1101-436634	169	25	.	.	.
10_1101-436634	170	1	RegTools	RegTools	NNP
10_1101-436634	170	2	identified	identify	VBD
10_1101-436634	170	3	a	a	DT
10_1101-436634	170	4	recurrent	recurrent	JJ
10_1101-436634	170	5	single	single	JJ
10_1101-436634	170	6	base	base	NN
10_1101-436634	170	7	pair	pair	NN
10_1101-436634	170	8	deletion	deletion	NN
10_1101-436634	170	9	that	that	WDT
10_1101-436634	170	10	results	result	VBZ
10_1101-436634	170	11	in	in	IN
10_1101-436634	170	12	an	an	DT
10_1101-436634	170	13	exon	exon	JJ
10_1101-436634	170	14	skipping	skipping	NN
10_1101-436634	170	15	event	event	NN
10_1101-436634	170	16	of	of	IN
10_1101-436634	170	17	exon	exon	NNP
10_1101-436634	170	18	8	8	CD
10_1101-436634	170	19	(	(	-LRB-
10_1101-436634	170	20	Supplementary	Supplementary	NNP
10_1101-436634	170	21	Figure	Figure	NNP
10_1101-436634	170	22	13	13	CD
10_1101-436634	170	23	)	)	-RRB-
10_1101-436634	170	24	.	.	.
10_1101-436634	171	1	This	this	DT
10_1101-436634	171	2	gene	gene	NN
10_1101-436634	171	3	is	be	VBZ
10_1101-436634	171	4	a	a	DT
10_1101-436634	171	5	paralog	paralog	NN
10_1101-436634	171	6	of	of	IN
10_1101-436634	171	7	RNF139	RNF139	NNP
10_1101-436634	171	8	,	,	,
10_1101-436634	171	9	which	which	WDT
10_1101-436634	171	10	has	have	VBZ
10_1101-436634	171	11	been	be	VBN
10_1101-436634	171	12	found	find	VBN
10_1101-436634	171	13	to	to	TO
10_1101-436634	171	14	be	be	VB
10_1101-436634	171	15	mutated	mutate	VBN
10_1101-436634	171	16	in	in	IN
10_1101-436634	171	17	several	several	JJ
10_1101-436634	171	18	cancer	cancer	NN
10_1101-436634	171	19	types41	types41	NN
10_1101-436634	171	20	.	.	.
10_1101-436634	172	1	This	this	DT
10_1101-436634	172	2	variant	variant	JJ
10_1101-436634	172	3	junction	junction	NN
10_1101-436634	172	4	association	association	NN
10_1101-436634	172	5	was	be	VBD
10_1101-436634	172	6	found	find	VBN
10_1101-436634	172	7	in	in	IN
10_1101-436634	172	8	STAD	STAD	NNP
10_1101-436634	172	9	,	,	,
10_1101-436634	172	10	UCEC	UCEC	NNP
10_1101-436634	172	11	,	,	,
10_1101-436634	172	12	COAD	COAD	NNP
10_1101-436634	172	13	,	,	,
10_1101-436634	172	14	and	and	CC
10_1101-436634	172	15	ESCA	esca	NN
10_1101-436634	172	16	tumors	tumor	NNS
10_1101-436634	172	17	,	,	,
10_1101-436634	172	18	all	all	DT
10_1101-436634	172	19	of	of	IN
10_1101-436634	172	20	which	which	WDT
10_1101-436634	172	21	are	be	VBP
10_1101-436634	172	22	considered	consider	VBN
10_1101-436634	172	23	to	to	TO
10_1101-436634	172	24	be	be	VB
10_1101-436634	172	25	MSI	MSI	NNP
10_1101-436634	172	26	-	-	HYPH
10_1101-436634	172	27	H	H	NNP
10_1101-436634	172	28	tumors36	tumors36	NN
10_1101-436634	172	29	.	.	.
10_1101-436634	173	1	After	after	IN
10_1101-436634	173	2	analyzing	analyze	VBG
10_1101-436634	173	3	the	the	DT
10_1101-436634	173	4	effect	effect	NN
10_1101-436634	173	5	of	of	IN
10_1101-436634	173	6	the	the	DT
10_1101-436634	173	7	exon	exon	JJ
10_1101-436634	173	8	skipping	skipping	NN
10_1101-436634	173	9	event	event	NN
10_1101-436634	173	10	on	on	IN
10_1101-436634	173	11	the	the	DT
10_1101-436634	173	12	mRNA	mrna	NN
10_1101-436634	173	13	sequence	sequence	NN
10_1101-436634	173	14	,	,	,
10_1101-436634	173	15	we	-PRON-	PRP
10_1101-436634	173	16	concluded	conclude	VBD
10_1101-436634	173	17	that	that	IN
10_1101-436634	173	18	the	the	DT
10_1101-436634	173	19	reading	reading	NN
10_1101-436634	173	20	frame	frame	NN
10_1101-436634	173	21	remains	remain	VBZ
10_1101-436634	173	22	intact	intact	JJ
10_1101-436634	173	23	,	,	,
10_1101-436634	173	24	possibly	possibly	RB
10_1101-436634	173	25	leading	lead	VBG
10_1101-436634	173	26	to	to	IN
10_1101-436634	173	27	a	a	DT
10_1101-436634	173	28	gain	gain	NN
10_1101-436634	173	29	of	of	IN
10_1101-436634	173	30	function	function	NN
10_1101-436634	173	31	event	event	NN
10_1101-436634	173	32	.	.	.
10_1101-436634	174	1	Additionally	additionally	RB
10_1101-436634	174	2	,	,	,
10_1101-436634	174	3	the	the	DT
10_1101-436634	174	4	skipping	skipping	NN
10_1101-436634	174	5	of	of	IN
10_1101-436634	174	6	exon	exon	NNP
10_1101-436634	174	7	8	8	CD
10_1101-436634	174	8	leads	lead	NNS
10_1101-436634	174	9	to	to	IN
10_1101-436634	174	10	the	the	DT
10_1101-436634	174	11	removal	removal	NN
10_1101-436634	174	12	of	of	IN
10_1101-436634	174	13	a	a	DT
10_1101-436634	174	14	transmembrane	transmembrane	JJ
10_1101-436634	174	15	domain	domain	NN
10_1101-436634	174	16	and	and	CC
10_1101-436634	174	17	a	a	DT
10_1101-436634	174	18	phosphorylation	phosphorylation	NN
10_1101-436634	174	19	site	site	NN
10_1101-436634	174	20	,	,	,
10_1101-436634	174	21	S352	s352	NN
10_1101-436634	174	22	,	,	,
10_1101-436634	174	23	which	which	WDT
10_1101-436634	174	24	could	could	MD
10_1101-436634	174	25	be	be	VB
10_1101-436634	174	26	important	important	JJ
10_1101-436634	174	27	for	for	IN
10_1101-436634	174	28	the	the	DT
10_1101-436634	174	29	regulation	regulation	NN
10_1101-436634	174	30	of	of	IN
10_1101-436634	174	31	this	this	DT
10_1101-436634	174	32	gene42	gene42	VBN
10_1101-436634	174	33	.	.	.
10_1101-436634	175	1	Based	base	VBN
10_1101-436634	175	2	on	on	IN
10_1101-436634	175	3	these	these	DT
10_1101-436634	175	4	findings	finding	NNS
10_1101-436634	175	5	,	,	,
10_1101-436634	175	6	RNF145	RNF145	NNP
10_1101-436634	175	7	may	may	MD
10_1101-436634	175	8	play	play	VB
10_1101-436634	175	9	a	a	DT
10_1101-436634	175	10	role	role	NN
10_1101-436634	175	11	similar	similar	JJ
10_1101-436634	175	12	to	to	IN
10_1101-436634	175	13	RNF139	RNF139	NNP
10_1101-436634	175	14	and	and	CC
10_1101-436634	175	15	may	may	MD
10_1101-436634	175	16	be	be	VB
10_1101-436634	175	17	an	an	DT
10_1101-436634	175	18	important	important	JJ
10_1101-436634	175	19	driver	driver	NN
10_1101-436634	175	20	event	event	NN
10_1101-436634	175	21	in	in	IN
10_1101-436634	175	22	certain	certain	JJ
10_1101-436634	175	23	tumor	tumor	NN
10_1101-436634	175	24	samples	sample	NNS
10_1101-436634	175	25	.	.	.
10_1101-436634	176	1	.CC	.CC	NFP
10_1101-436634	176	2	-	-	:
10_1101-436634	176	3	BY	by	IN
10_1101-436634	176	4	-	-	HYPH
10_1101-436634	176	5	NC	NC	NNP
10_1101-436634	176	6	-	-	HYPH
10_1101-436634	176	7	ND	ND	NNP
10_1101-436634	176	8	4.0	4.0	CD
10_1101-436634	176	9	International	international	JJ
10_1101-436634	176	10	licensea	licensea	NNS
10_1101-436634	176	11	certified	certify	VBN
10_1101-436634	176	12	by	by	IN
10_1101-436634	176	13	peer	peer	NN
10_1101-436634	176	14	review	review	NN
10_1101-436634	176	15	)	)	-RRB-
10_1101-436634	176	16	is	be	VBZ
10_1101-436634	176	17	the	the	DT
10_1101-436634	176	18	author	author	NN
10_1101-436634	176	19	/	/	SYM
10_1101-436634	176	20	funder	funder	NN
10_1101-436634	176	21	,	,	,
10_1101-436634	176	22	who	who	WP
10_1101-436634	176	23	has	have	VBZ
10_1101-436634	176	24	granted	grant	VBN
10_1101-436634	176	25	bioRxiv	biorxiv	IN
10_1101-436634	176	26	a	a	DT
10_1101-436634	176	27	license	license	NN
10_1101-436634	176	28	to	to	TO
10_1101-436634	176	29	display	display	VB
10_1101-436634	176	30	the	the	DT
10_1101-436634	176	31	preprint	preprint	NN
10_1101-436634	176	32	in	in	IN
10_1101-436634	176	33	perpetuity	perpetuity	NN
10_1101-436634	176	34	.	.	.
10_1101-436634	177	1	It	-PRON-	PRP
10_1101-436634	177	2	is	be	VBZ
10_1101-436634	177	3	made	make	VBN
10_1101-436634	177	4	available	available	JJ
10_1101-436634	177	5	under	under	IN
10_1101-436634	177	6	The	the	DT
10_1101-436634	177	7	copyright	copyright	NN
10_1101-436634	177	8	holder	holder	NN
10_1101-436634	177	9	for	for	IN
10_1101-436634	177	10	this	this	DT
10_1101-436634	177	11	preprint	preprint	NN
10_1101-436634	177	12	(	(	-LRB-
10_1101-436634	177	13	which	which	WDT
10_1101-436634	177	14	was	be	VBD
10_1101-436634	177	15	notthis	notthis	DT
10_1101-436634	177	16	version	version	NN
10_1101-436634	177	17	posted	post	VBN
10_1101-436634	177	18	January	January	NNP
10_1101-436634	177	19	5	5	CD
10_1101-436634	177	20	,	,	,
10_1101-436634	177	21	2021	2021	CD
10_1101-436634	177	22	.	.	.
10_1101-436634	177	23	;	;	:
10_1101-436634	177	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	177	25	:	:	:
10_1101-436634	177	26	bioRxiv	biorxiv	VB
10_1101-436634	177	27	preprint	preprint	NN
10_1101-436634	177	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	177	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	177	30	9	9	CD
10_1101-436634	177	31	While	while	IN
10_1101-436634	177	32	most	most	JJS
10_1101-436634	177	33	of	of	IN
10_1101-436634	177	34	our	-PRON-	PRP$
10_1101-436634	177	35	analysis	analysis	NN
10_1101-436634	177	36	focused	focus	VBN
10_1101-436634	177	37	on	on	IN
10_1101-436634	177	38	splice	splice	NN
10_1101-436634	177	39	altering	altering	NN
10_1101-436634	177	40	variants	variant	NNS
10_1101-436634	177	41	that	that	WDT
10_1101-436634	177	42	resulted	result	VBD
10_1101-436634	177	43	in	in	IN
10_1101-436634	177	44	D	d	NN
10_1101-436634	177	45	,	,	,
10_1101-436634	177	46	A	A	NNP
10_1101-436634	177	47	,	,	,
10_1101-436634	177	48	NDA	NDA	NNP
10_1101-436634	177	49	junctions	junction	NNS
10_1101-436634	177	50	,	,	,
10_1101-436634	177	51	we	-PRON-	PRP
10_1101-436634	177	52	also	also	RB
10_1101-436634	177	53	wanted	want	VBD
10_1101-436634	177	54	to	to	TO
10_1101-436634	177	55	investigate	investigate	VB
10_1101-436634	177	56	variants	variant	NNS
10_1101-436634	177	57	that	that	WDT
10_1101-436634	177	58	shifted	shift	VBD
10_1101-436634	177	59	the	the	DT
10_1101-436634	177	60	usage	usage	NN
10_1101-436634	177	61	of	of	IN
10_1101-436634	177	62	known	know	VBN
10_1101-436634	177	63	donor	donor	NN
10_1101-436634	177	64	and	and	CC
10_1101-436634	177	65	acceptor	acceptor	NN
10_1101-436634	177	66	sites	site	NNS
10_1101-436634	177	67	.	.	.
10_1101-436634	178	1	Through	through	IN
10_1101-436634	178	2	this	this	DT
10_1101-436634	178	3	analysis	analysis	NN
10_1101-436634	178	4	,	,	,
10_1101-436634	178	5	we	-PRON-	PRP
10_1101-436634	178	6	identified	identify	VBD
10_1101-436634	178	7	CDKN2A	CDKN2A	NNP
10_1101-436634	178	8	,	,	,
10_1101-436634	178	9	a	a	DT
10_1101-436634	178	10	tumor	tumor	NN
10_1101-436634	178	11	suppressor	suppressor	NN
10_1101-436634	178	12	gene	gene	NN
10_1101-436634	178	13	that	that	WDT
10_1101-436634	178	14	is	be	VBZ
10_1101-436634	178	15	frequently	frequently	RB
10_1101-436634	178	16	mutated	mutate	VBN
10_1101-436634	178	17	in	in	IN
10_1101-436634	178	18	numerous	numerous	JJ
10_1101-436634	178	19	cancers43	cancers43	NNP
10_1101-436634	178	20	,	,	,
10_1101-436634	178	21	to	to	TO
10_1101-436634	178	22	have	have	VB
10_1101-436634	178	23	several	several	JJ
10_1101-436634	178	24	variants	variant	NNS
10_1101-436634	178	25	that	that	WDT
10_1101-436634	178	26	led	lead	VBD
10_1101-436634	178	27	to	to	IN
10_1101-436634	178	28	alternate	alternate	JJ
10_1101-436634	178	29	donor	donor	NN
10_1101-436634	178	30	usage	usage	NN
10_1101-436634	178	31	(	(	-LRB-
10_1101-436634	178	32	Supplementary	Supplementary	NNP
10_1101-436634	178	33	Figure	Figure	NNP
10_1101-436634	178	34	14	14	CD
10_1101-436634	178	35	)	)	-RRB-
10_1101-436634	178	36	.	.	.
10_1101-436634	179	1	When	when	WRB
10_1101-436634	179	2	these	these	DT
10_1101-436634	179	3	variants	variant	NNS
10_1101-436634	179	4	are	be	VBP
10_1101-436634	179	5	present	present	JJ
10_1101-436634	179	6	,	,	,
10_1101-436634	179	7	an	an	DT
10_1101-436634	179	8	alternate	alternate	RB
10_1101-436634	179	9	known	know	VBN
10_1101-436634	179	10	donor	donor	NN
10_1101-436634	179	11	site	site	NN
10_1101-436634	179	12	is	be	VBZ
10_1101-436634	179	13	used	use	VBN
10_1101-436634	179	14	that	that	WDT
10_1101-436634	179	15	leads	lead	VBZ
10_1101-436634	179	16	to	to	IN
10_1101-436634	179	17	the	the	DT
10_1101-436634	179	18	formation	formation	NN
10_1101-436634	179	19	of	of	IN
10_1101-436634	179	20	the	the	DT
10_1101-436634	179	21	transcript	transcript	NN
10_1101-436634	179	22	ENST00000579122.1	ENST00000579122.1	VBD
10_1101-436634	179	23	instead	instead	RB
10_1101-436634	179	24	of	of	IN
10_1101-436634	179	25	ENST00000304494.9	enst00000304494.9	NN
10_1101-436634	179	26	,	,	,
10_1101-436634	179	27	the	the	DT
10_1101-436634	179	28	transcript	transcript	NN
10_1101-436634	179	29	that	that	WDT
10_1101-436634	179	30	encodes	encode	VBZ
10_1101-436634	179	31	for	for	IN
10_1101-436634	179	32	p16ink4a	p16ink4a	NNP
10_1101-436634	179	33	,	,	,
10_1101-436634	179	34	a	a	DT
10_1101-436634	179	35	known	know	VBN
10_1101-436634	179	36	tumor	tumor	NN
10_1101-436634	179	37	suppressor	suppressor	NN
10_1101-436634	179	38	.	.	.
10_1101-436634	180	1	The	the	DT
10_1101-436634	180	2	transcript	transcript	NN
10_1101-436634	180	3	that	that	WDT
10_1101-436634	180	4	results	result	VBZ
10_1101-436634	180	5	from	from	IN
10_1101-436634	180	6	use	use	NN
10_1101-436634	180	7	of	of	IN
10_1101-436634	180	8	this	this	DT
10_1101-436634	180	9	alternate	alternate	JJ
10_1101-436634	180	10	donor	donor	NN
10_1101-436634	180	11	site	site	NN
10_1101-436634	180	12	is	be	VBZ
10_1101-436634	180	13	missing	miss	VBG
10_1101-436634	180	14	the	the	DT
10_1101-436634	180	15	last	last	JJ
10_1101-436634	180	16	twenty	twenty	CD
10_1101-436634	180	17	-	-	HYPH
10_1101-436634	180	18	eight	eight	CD
10_1101-436634	180	19	amino	amino	JJ
10_1101-436634	180	20	acids	acid	NNS
10_1101-436634	180	21	that	that	WDT
10_1101-436634	180	22	form	form	VBP
10_1101-436634	180	23	the	the	DT
10_1101-436634	180	24	C	c	NN
10_1101-436634	180	25	-	-	HYPH
10_1101-436634	180	26	terminal	terminal	JJ
10_1101-436634	180	27	end	end	NN
10_1101-436634	180	28	of	of	IN
10_1101-436634	180	29	p16ink4a	p16ink4a	RB
10_1101-436634	180	30	.	.	.
10_1101-436634	181	1	Notably	notably	RB
10_1101-436634	181	2	,	,	,
10_1101-436634	181	3	this	this	DT
10_1101-436634	181	4	removes	remove	VBZ
10_1101-436634	181	5	two	two	CD
10_1101-436634	181	6	phosphorylation	phosphorylation	NN
10_1101-436634	181	7	sites	site	NNS
10_1101-436634	181	8	within	within	IN
10_1101-436634	181	9	the	the	DT
10_1101-436634	181	10	p16	p16	NN
10_1101-436634	181	11	protein	protein	NN
10_1101-436634	181	12	,	,	,
10_1101-436634	181	13	S140	S140	NNP
10_1101-436634	181	14	and	and	CC
10_1101-436634	181	15	S152	S152	NNP
10_1101-436634	181	16	,	,	,
10_1101-436634	181	17	which	which	WDT
10_1101-436634	181	18	when	when	WRB
10_1101-436634	181	19	phosphorylated	phosphorylate	VBD
10_1101-436634	181	20	promotes	promote	VBZ
10_1101-436634	181	21	the	the	DT
10_1101-436634	181	22	association	association	NN
10_1101-436634	181	23	of	of	IN
10_1101-436634	181	24	p16ink4a	p16ink4a	NNP
10_1101-436634	181	25	with	with	IN
10_1101-436634	181	26	CDK444	CDK444	NNP
10_1101-436634	181	27	.	.	.
10_1101-436634	182	1	This	this	DT
10_1101-436634	182	2	finding	finding	NN
10_1101-436634	182	3	highlights	highlight	VBZ
10_1101-436634	182	4	the	the	DT
10_1101-436634	182	5	importance	importance	NN
10_1101-436634	182	6	of	of	IN
10_1101-436634	182	7	including	include	VBG
10_1101-436634	182	8	known	know	VBN
10_1101-436634	182	9	transcripts	transcript	NNS
10_1101-436634	182	10	in	in	IN
10_1101-436634	182	11	alternative	alternative	JJ
10_1101-436634	182	12	splicing	splicing	NN
10_1101-436634	182	13	analyses	analysis	NNS
10_1101-436634	182	14	as	as	IN
10_1101-436634	182	15	variants	variant	NNS
10_1101-436634	182	16	may	may	MD
10_1101-436634	182	17	alter	alter	VB
10_1101-436634	182	18	splice	splice	NN
10_1101-436634	182	19	site	site	NN
10_1101-436634	182	20	usage	usage	NN
10_1101-436634	182	21	in	in	IN
10_1101-436634	182	22	a	a	DT
10_1101-436634	182	23	way	way	NN
10_1101-436634	182	24	that	that	WDT
10_1101-436634	182	25	results	result	VBZ
10_1101-436634	182	26	in	in	IN
10_1101-436634	182	27	a	a	DT
10_1101-436634	182	28	known	known	JJ
10_1101-436634	182	29	but	but	CC
10_1101-436634	182	30	pathogenic	pathogenic	JJ
10_1101-436634	182	31	transcript	transcript	NN
10_1101-436634	182	32	product	product	NN
10_1101-436634	182	33	.	.	.
10_1101-436634	183	1	Discussion	Discussion	NNP
10_1101-436634	183	2	Splice	Splice	NNP
10_1101-436634	183	3	associated	associate	VBD
10_1101-436634	183	4	variants	variant	NNS
10_1101-436634	183	5	are	be	VBP
10_1101-436634	183	6	often	often	RB
10_1101-436634	183	7	overlooked	overlook	VBN
10_1101-436634	183	8	in	in	IN
10_1101-436634	183	9	traditional	traditional	JJ
10_1101-436634	183	10	genomic	genomic	JJ
10_1101-436634	183	11	analysis	analysis	NN
10_1101-436634	183	12	.	.	.
10_1101-436634	184	1	To	to	TO
10_1101-436634	184	2	address	address	VB
10_1101-436634	184	3	this	this	DT
10_1101-436634	184	4	limitation	limitation	NN
10_1101-436634	184	5	,	,	,
10_1101-436634	184	6	we	-PRON-	PRP
10_1101-436634	184	7	created	create	VBD
10_1101-436634	184	8	RegTools	RegTools	NNP
10_1101-436634	184	9	,	,	,
10_1101-436634	184	10	a	a	DT
10_1101-436634	184	11	software	software	NN
10_1101-436634	184	12	suite	suite	NN
10_1101-436634	184	13	for	for	IN
10_1101-436634	184	14	the	the	DT
10_1101-436634	184	15	analysis	analysis	NN
10_1101-436634	184	16	of	of	IN
10_1101-436634	184	17	variants	variant	NNS
10_1101-436634	184	18	and	and	CC
10_1101-436634	184	19	junctions	junction	NNS
10_1101-436634	184	20	in	in	IN
10_1101-436634	184	21	a	a	DT
10_1101-436634	184	22	splicing	splicing	NN
10_1101-436634	184	23	context	context	NN
10_1101-436634	184	24	.	.	.
10_1101-436634	185	1	By	by	IN
10_1101-436634	185	2	relying	rely	VBG
10_1101-436634	185	3	on	on	IN
10_1101-436634	185	4	well	well	RB
10_1101-436634	185	5	-	-	HYPH
10_1101-436634	185	6	established	establish	VBN
10_1101-436634	185	7	standards	standard	NNS
10_1101-436634	185	8	for	for	IN
10_1101-436634	185	9	analyzing	analyze	VBG
10_1101-436634	185	10	genomic	genomic	JJ
10_1101-436634	185	11	and	and	CC
10_1101-436634	185	12	transcriptomic	transcriptomic	JJ
10_1101-436634	185	13	data	datum	NNS
10_1101-436634	185	14	and	and	CC
10_1101-436634	185	15	allowing	allow	VBG
10_1101-436634	185	16	flexible	flexible	JJ
10_1101-436634	185	17	analysis	analysis	NN
10_1101-436634	185	18	parameters	parameter	NNS
10_1101-436634	185	19	,	,	,
10_1101-436634	185	20	we	-PRON-	PRP
10_1101-436634	185	21	enable	enable	VBP
10_1101-436634	185	22	users	user	NNS
10_1101-436634	185	23	to	to	TO
10_1101-436634	185	24	apply	apply	VB
10_1101-436634	185	25	RegTools	RegTools	NNP
10_1101-436634	185	26	to	to	IN
10_1101-436634	185	27	a	a	DT
10_1101-436634	185	28	wide	wide	JJ
10_1101-436634	185	29	set	set	NN
10_1101-436634	185	30	of	of	IN
10_1101-436634	185	31	scientific	scientific	JJ
10_1101-436634	185	32	methodologies	methodology	NNS
10_1101-436634	185	33	and	and	CC
10_1101-436634	185	34	datasets	dataset	NNS
10_1101-436634	185	35	.	.	.
10_1101-436634	186	1	To	to	TO
10_1101-436634	186	2	ease	ease	VB
10_1101-436634	186	3	the	the	DT
10_1101-436634	186	4	use	use	NN
10_1101-436634	186	5	and	and	CC
10_1101-436634	186	6	integration	integration	NN
10_1101-436634	186	7	of	of	IN
10_1101-436634	186	8	RegTools	RegTools	NNP
10_1101-436634	186	9	into	into	IN
10_1101-436634	186	10	analysis	analysis	NN
10_1101-436634	186	11	workflows	workflow	NNS
10_1101-436634	186	12	,	,	,
10_1101-436634	186	13	we	-PRON-	PRP
10_1101-436634	186	14	provide	provide	VBP
10_1101-436634	186	15	documentation	documentation	NN
10_1101-436634	186	16	and	and	CC
10_1101-436634	186	17	example	example	NN
10_1101-436634	186	18	workflows	workflow	NNS
10_1101-436634	186	19	via	via	IN
10_1101-436634	186	20	(	(	-LRB-
10_1101-436634	186	21	regtools.org	regtools.org	CD
10_1101-436634	186	22	)	)	-RRB-
10_1101-436634	186	23	and	and	CC
10_1101-436634	186	24	provide	provide	VB
10_1101-436634	186	25	a	a	DT
10_1101-436634	186	26	Docker	Docker	NNP
10_1101-436634	186	27	image	image	NN
10_1101-436634	186	28	with	with	IN
10_1101-436634	186	29	all	all	DT
10_1101-436634	186	30	necessary	necessary	JJ
10_1101-436634	186	31	software	software	NN
10_1101-436634	186	32	installed	instal	VBN
10_1101-436634	186	33	.	.	.
10_1101-436634	187	1	In	in	IN
10_1101-436634	187	2	order	order	NN
10_1101-436634	187	3	to	to	TO
10_1101-436634	187	4	demonstrate	demonstrate	VB
10_1101-436634	187	5	the	the	DT
10_1101-436634	187	6	utility	utility	NN
10_1101-436634	187	7	of	of	IN
10_1101-436634	187	8	our	-PRON-	PRP$
10_1101-436634	187	9	tool	tool	NN
10_1101-436634	187	10	,	,	,
10_1101-436634	187	11	we	-PRON-	PRP
10_1101-436634	187	12	applied	apply	VBD
10_1101-436634	187	13	RegTools	RegTools	NNP
10_1101-436634	187	14	to	to	IN
10_1101-436634	187	15	9,173	9,173	CD
10_1101-436634	187	16	tumor	tumor	NN
10_1101-436634	187	17	samples	sample	NNS
10_1101-436634	187	18	across	across	IN
10_1101-436634	187	19	35	35	CD
10_1101-436634	187	20	tumor	tumor	NN
10_1101-436634	187	21	types	type	NNS
10_1101-436634	187	22	to	to	TO
10_1101-436634	187	23	profile	profile	VB
10_1101-436634	187	24	the	the	DT
10_1101-436634	187	25	landscape	landscape	NN
10_1101-436634	187	26	of	of	IN
10_1101-436634	187	27	this	this	DT
10_1101-436634	187	28	category	category	NN
10_1101-436634	187	29	of	of	IN
10_1101-436634	187	30	variants	variant	NNS
10_1101-436634	187	31	.	.	.
10_1101-436634	188	1	From	from	IN
10_1101-436634	188	2	this	this	DT
10_1101-436634	188	3	analysis	analysis	NN
10_1101-436634	188	4	,	,	,
10_1101-436634	188	5	we	-PRON-	PRP
10_1101-436634	188	6	report	report	VBP
10_1101-436634	188	7	133,987	133,987	CD
10_1101-436634	188	8	variants	variant	NNS
10_1101-436634	188	9	that	that	WDT
10_1101-436634	188	10	cause	cause	VBP
10_1101-436634	188	11	novel	novel	NN
10_1101-436634	188	12	splicing	splicing	NN
10_1101-436634	188	13	events	event	NNS
10_1101-436634	188	14	that	that	WDT
10_1101-436634	188	15	were	be	VBD
10_1101-436634	188	16	missed	miss	VBN
10_1101-436634	188	17	by	by	IN
10_1101-436634	188	18	VEP	VEP	NNP
10_1101-436634	188	19	or	or	CC
10_1101-436634	188	20	SpliceAI	SpliceAI	NNP
10_1101-436634	188	21	.	.	.
10_1101-436634	189	1	Only	only	RB
10_1101-436634	189	2	1.4	1.4	CD
10_1101-436634	189	3	percent	percent	NN
10_1101-436634	189	4	of	of	IN
10_1101-436634	189	5	these	these	DT
10_1101-436634	189	6	mutations	mutation	NNS
10_1101-436634	189	7	were	be	VBD
10_1101-436634	189	8	previously	previously	RB
10_1101-436634	189	9	discovered	discover	VBN
10_1101-436634	189	10	by	by	IN
10_1101-436634	189	11	similar	similar	JJ
10_1101-436634	189	12	attempts	attempt	NNS
10_1101-436634	189	13	,	,	,
10_1101-436634	189	14	while	while	IN
10_1101-436634	189	15	98.6	98.6	CD
10_1101-436634	189	16	percent	percent	NN
10_1101-436634	189	17	are	be	VBP
10_1101-436634	189	18	novel	novel	JJ
10_1101-436634	189	19	findings	finding	NNS
10_1101-436634	189	20	.	.	.
10_1101-436634	190	1	We	-PRON-	PRP
10_1101-436634	190	2	demonstrate	demonstrate	VBP
10_1101-436634	190	3	that	that	IN
10_1101-436634	190	4	there	there	EX
10_1101-436634	190	5	are	be	VBP
10_1101-436634	190	6	splice	splice	NN
10_1101-436634	190	7	altering	alter	VBG
10_1101-436634	190	8	variants	variant	NNS
10_1101-436634	190	9	that	that	WDT
10_1101-436634	190	10	occur	occur	VBP
10_1101-436634	190	11	beyond	beyond	IN
10_1101-436634	190	12	the	the	DT
10_1101-436634	190	13	splice	splice	NN
10_1101-436634	190	14	site	site	NN
10_1101-436634	190	15	consensus	consensus	NN
10_1101-436634	190	16	sequence	sequence	NN
10_1101-436634	190	17	,	,	,
10_1101-436634	190	18	shift	shift	NN
10_1101-436634	190	19	transcript	transcript	NN
10_1101-436634	190	20	usage	usage	NN
10_1101-436634	190	21	between	between	IN
10_1101-436634	190	22	known	know	VBN
10_1101-436634	190	23	transcripts	transcript	NNS
10_1101-436634	190	24	,	,	,
10_1101-436634	190	25	and	and	CC
10_1101-436634	190	26	create	create	VB
10_1101-436634	190	27	novel	novel	JJ
10_1101-436634	190	28	exon	exon	NN
10_1101-436634	190	29	-	-	HYPH
10_1101-436634	190	30	exon	exon	NN
10_1101-436634	190	31	junctions	junction	NNS
10_1101-436634	190	32	that	that	WDT
10_1101-436634	190	33	have	have	VBP
10_1101-436634	190	34	not	not	RB
10_1101-436634	190	35	been	be	VBN
10_1101-436634	190	36	previously	previously	RB
10_1101-436634	190	37	described	describe	VBN
10_1101-436634	190	38	.	.	.
10_1101-436634	191	1	Specifically	specifically	RB
10_1101-436634	191	2	,	,	,
10_1101-436634	191	3	we	-PRON-	PRP
10_1101-436634	191	4	describe	describe	VBP
10_1101-436634	191	5	notable	notable	JJ
10_1101-436634	191	6	findings	finding	NNS
10_1101-436634	191	7	within	within	IN
10_1101-436634	191	8	B2	B2	NNP
10_1101-436634	191	9	M	M	NNP
10_1101-436634	191	10	,	,	,
10_1101-436634	191	11	RNF145	RNF145	NNP
10_1101-436634	191	12	,	,	,
10_1101-436634	191	13	and	and	CC
10_1101-436634	191	14	CDKN2A.	CDKN2A.	NNP
10_1101-436634	192	1	These	these	DT
10_1101-436634	192	2	results	result	NNS
10_1101-436634	192	3	demonstrate	demonstrate	VBP
10_1101-436634	192	4	the	the	DT
10_1101-436634	192	5	utility	utility	NN
10_1101-436634	192	6	of	of	IN
10_1101-436634	192	7	RegTools	RegTools	NNP
10_1101-436634	192	8	in	in	IN
10_1101-436634	192	9	discovering	discover	VBG
10_1101-436634	192	10	novel	novel	JJ
10_1101-436634	192	11	splice	splice	NN
10_1101-436634	192	12	-	-	HYPH
10_1101-436634	192	13	altering	alter	VBG
10_1101-436634	192	14	mutations	mutation	NNS
10_1101-436634	192	15	and	and	CC
10_1101-436634	192	16	confirm	confirm	VB
10_1101-436634	192	17	the	the	DT
10_1101-436634	192	18	importance	importance	NN
10_1101-436634	192	19	of	of	IN
10_1101-436634	192	20	integrating	integrate	VBG
10_1101-436634	192	21	RNA	RNA	NNP
10_1101-436634	192	22	and	and	CC
10_1101-436634	192	23	DNA	DNA	NNP
10_1101-436634	192	24	sequencing	sequencing	NN
10_1101-436634	192	25	data	datum	NNS
10_1101-436634	192	26	in	in	IN
10_1101-436634	192	27	understanding	understand	VBG
10_1101-436634	192	28	the	the	DT
10_1101-436634	192	29	consequences	consequence	NNS
10_1101-436634	192	30	of	of	IN
10_1101-436634	192	31	somatic	somatic	JJ
10_1101-436634	192	32	mutations	mutation	NNS
10_1101-436634	192	33	in	in	IN
10_1101-436634	192	34	cancer	cancer	NN
10_1101-436634	192	35	.	.	.
10_1101-436634	193	1	To	to	TO
10_1101-436634	193	2	allow	allow	VB
10_1101-436634	193	3	further	further	JJ
10_1101-436634	193	4	investigation	investigation	NN
10_1101-436634	193	5	of	of	IN
10_1101-436634	193	6	these	these	DT
10_1101-436634	193	7	identified	identify	VBN
10_1101-436634	193	8	events	event	NNS
10_1101-436634	193	9	,	,	,
10_1101-436634	193	10	we	-PRON-	PRP
10_1101-436634	193	11	make	make	VBP
10_1101-436634	193	12	all	all	DT
10_1101-436634	193	13	of	of	IN
10_1101-436634	193	14	our	-PRON-	PRP$
10_1101-436634	193	15	annotated	annotated	JJ
10_1101-436634	193	16	result	result	NN
10_1101-436634	193	17	files	file	NNS
10_1101-436634	193	18	(	(	-LRB-
10_1101-436634	193	19	Supplemental	supplemental	JJ
10_1101-436634	193	20	Files	Files	NNP
10_1101-436634	193	21	1	1	CD
10_1101-436634	193	22	-	-	SYM
10_1101-436634	193	23	4	4	CD
10_1101-436634	193	24	)	)	-RRB-
10_1101-436634	193	25	and	and	CC
10_1101-436634	193	26	recurrence	recurrence	VB
10_1101-436634	193	27	analysis	analysis	NN
10_1101-436634	193	28	files	file	NNS
10_1101-436634	193	29	(	(	-LRB-
10_1101-436634	193	30	Supplemental	supplemental	JJ
10_1101-436634	193	31	Files	Files	NNP
10_1101-436634	193	32	5	5	CD
10_1101-436634	193	33	-	-	SYM
10_1101-436634	193	34	6	6	CD
10_1101-436634	193	35	)	)	-RRB-
10_1101-436634	193	36	available	available	JJ
10_1101-436634	193	37	.	.	.
10_1101-436634	194	1	Understanding	understand	VBG
10_1101-436634	194	2	the	the	DT
10_1101-436634	194	3	splicing	splicing	NN
10_1101-436634	194	4	landscape	landscape	NN
10_1101-436634	194	5	is	be	VBZ
10_1101-436634	194	6	crucial	crucial	JJ
10_1101-436634	194	7	for	for	IN
10_1101-436634	194	8	unlocking	unlock	VBG
10_1101-436634	194	9	potential	potential	JJ
10_1101-436634	194	10	therapeutic	therapeutic	JJ
10_1101-436634	194	11	avenues	avenue	NNS
10_1101-436634	194	12	in	in	IN
10_1101-436634	194	13	precision	precision	NN
10_1101-436634	194	14	medicine	medicine	NN
10_1101-436634	194	15	and	and	CC
10_1101-436634	194	16	elucidating	elucidate	VBG
10_1101-436634	194	17	the	the	DT
10_1101-436634	194	18	basic	basic	JJ
10_1101-436634	194	19	mechanisms	mechanism	NNS
10_1101-436634	194	20	of	of	IN
10_1101-436634	194	21	splicing	splicing	NN
10_1101-436634	194	22	.	.	.
10_1101-436634	195	1	The	the	DT
10_1101-436634	195	2	exploration	exploration	NN
10_1101-436634	195	3	of	of	IN
10_1101-436634	195	4	novel	novel	JJ
10_1101-436634	195	5	tumor	tumor	NN
10_1101-436634	195	6	-	-	HYPH
10_1101-436634	195	7	specific	specific	JJ
10_1101-436634	195	8	junctions	junction	NNS
10_1101-436634	195	9	will	will	MD
10_1101-436634	195	10	undoubtedly	undoubtedly	RB
10_1101-436634	195	11	lead	lead	VB
10_1101-436634	195	12	to	to	IN
10_1101-436634	195	13	translational	translational	JJ
10_1101-436634	195	14	applications	application	NNS
10_1101-436634	195	15	,	,	,
10_1101-436634	195	16	from	from	IN
10_1101-436634	195	17	discovering	discover	VBG
10_1101-436634	195	18	novel	novel	JJ
10_1101-436634	195	19	tumor	tumor	NN
10_1101-436634	195	20	drivers	driver	NNS
10_1101-436634	195	21	,	,	,
10_1101-436634	195	22	diagnostic	diagnostic	JJ
10_1101-436634	195	23	and	and	CC
10_1101-436634	195	24	prognostic	prognostic	JJ
10_1101-436634	195	25	biomarkers	biomarker	NNS
10_1101-436634	195	26	,	,	,
10_1101-436634	195	27	and	and	CC
10_1101-436634	195	28	drug	drug	NN
10_1101-436634	195	29	targets	target	NNS
10_1101-436634	195	30	,	,	,
10_1101-436634	195	31	to	to	IN
10_1101-436634	195	32	identifying	identify	VBG
10_1101-436634	195	33	a	a	DT
10_1101-436634	195	34	previously	previously	RB
10_1101-436634	195	35	untapped	untapped	JJ
10_1101-436634	195	36	source	source	NN
10_1101-436634	195	37	of	of	IN
10_1101-436634	195	38	neoantigens	neoantigen	NNS
10_1101-436634	195	39	for	for	IN
10_1101-436634	195	40	personalized	personalized	JJ
10_1101-436634	195	41	immunotherapy	immunotherapy	NN
10_1101-436634	195	42	.	.	.
10_1101-436634	196	1	While	while	IN
10_1101-436634	196	2	our	-PRON-	PRP$
10_1101-436634	196	3	analysis	analysis	NN
10_1101-436634	196	4	.CC	.CC	NFP
10_1101-436634	196	5	-	-	:
10_1101-436634	196	6	BY	by	IN
10_1101-436634	196	7	-	-	HYPH
10_1101-436634	196	8	NC	NC	NNP
10_1101-436634	196	9	-	-	HYPH
10_1101-436634	196	10	ND	ND	NNP
10_1101-436634	196	11	4.0	4.0	CD
10_1101-436634	196	12	International	international	JJ
10_1101-436634	196	13	licensea	licensea	NNS
10_1101-436634	196	14	certified	certify	VBN
10_1101-436634	196	15	by	by	IN
10_1101-436634	196	16	peer	peer	NN
10_1101-436634	196	17	review	review	NN
10_1101-436634	196	18	)	)	-RRB-
10_1101-436634	196	19	is	be	VBZ
10_1101-436634	196	20	the	the	DT
10_1101-436634	196	21	author	author	NN
10_1101-436634	196	22	/	/	SYM
10_1101-436634	196	23	funder	funder	NN
10_1101-436634	196	24	,	,	,
10_1101-436634	196	25	who	who	WP
10_1101-436634	196	26	has	have	VBZ
10_1101-436634	196	27	granted	grant	VBN
10_1101-436634	196	28	bioRxiv	biorxiv	IN
10_1101-436634	196	29	a	a	DT
10_1101-436634	196	30	license	license	NN
10_1101-436634	196	31	to	to	TO
10_1101-436634	196	32	display	display	VB
10_1101-436634	196	33	the	the	DT
10_1101-436634	196	34	preprint	preprint	NN
10_1101-436634	196	35	in	in	IN
10_1101-436634	196	36	perpetuity	perpetuity	NN
10_1101-436634	196	37	.	.	.
10_1101-436634	197	1	It	-PRON-	PRP
10_1101-436634	197	2	is	be	VBZ
10_1101-436634	197	3	made	make	VBN
10_1101-436634	197	4	available	available	JJ
10_1101-436634	197	5	under	under	IN
10_1101-436634	197	6	The	the	DT
10_1101-436634	197	7	copyright	copyright	NN
10_1101-436634	197	8	holder	holder	NN
10_1101-436634	197	9	for	for	IN
10_1101-436634	197	10	this	this	DT
10_1101-436634	197	11	preprint	preprint	NN
10_1101-436634	197	12	(	(	-LRB-
10_1101-436634	197	13	which	which	WDT
10_1101-436634	197	14	was	be	VBD
10_1101-436634	197	15	notthis	notthis	DT
10_1101-436634	197	16	version	version	NN
10_1101-436634	197	17	posted	post	VBN
10_1101-436634	197	18	January	January	NNP
10_1101-436634	197	19	5	5	CD
10_1101-436634	197	20	,	,	,
10_1101-436634	197	21	2021	2021	CD
10_1101-436634	197	22	.	.	.
10_1101-436634	197	23	;	;	:
10_1101-436634	197	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	197	25	:	:	:
10_1101-436634	197	26	bioRxiv	biorxiv	VB
10_1101-436634	197	27	preprint	preprint	NN
10_1101-436634	197	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	197	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NFP
10_1101-436634	197	30	10	10	CD
10_1101-436634	197	31	focuses	focus	NNS
10_1101-436634	197	32	on	on	IN
10_1101-436634	197	33	splice	splice	NN
10_1101-436634	197	34	altering	altering	NN
10_1101-436634	197	35	variants	variant	NNS
10_1101-436634	197	36	within	within	IN
10_1101-436634	197	37	cancers	cancer	NNS
10_1101-436634	197	38	,	,	,
10_1101-436634	197	39	we	-PRON-	PRP
10_1101-436634	197	40	believe	believe	VBP
10_1101-436634	197	41	RegTools	RegTools	NNP
10_1101-436634	197	42	will	will	MD
10_1101-436634	197	43	play	play	VB
10_1101-436634	197	44	an	an	DT
10_1101-436634	197	45	important	important	JJ
10_1101-436634	197	46	role	role	NN
10_1101-436634	197	47	in	in	IN
10_1101-436634	197	48	answering	answer	VBG
10_1101-436634	197	49	this	this	DT
10_1101-436634	197	50	broad	broad	JJ
10_1101-436634	197	51	range	range	NN
10_1101-436634	197	52	of	of	IN
10_1101-436634	197	53	questions	question	NNS
10_1101-436634	197	54	by	by	IN
10_1101-436634	197	55	helping	help	VBG
10_1101-436634	197	56	users	user	NNS
10_1101-436634	197	57	extract	extract	VB
10_1101-436634	197	58	splicing	splice	VBG
10_1101-436634	197	59	information	information	NN
10_1101-436634	197	60	from	from	IN
10_1101-436634	197	61	transcriptome	transcriptome	DT
10_1101-436634	197	62	data	datum	NNS
10_1101-436634	197	63	and	and	CC
10_1101-436634	197	64	linking	link	VBG
10_1101-436634	197	65	it	-PRON-	PRP
10_1101-436634	197	66	to	to	IN
10_1101-436634	197	67	somatic	somatic	VB
10_1101-436634	197	68	(	(	-LRB-
10_1101-436634	197	69	or	or	CC
10_1101-436634	197	70	germline	germline	NN
10_1101-436634	197	71	)	)	-RRB-
10_1101-436634	197	72	variant	variant	JJ
10_1101-436634	197	73	calls	call	NNS
10_1101-436634	197	74	.	.	.
10_1101-436634	198	1	The	the	DT
10_1101-436634	198	2	computational	computational	JJ
10_1101-436634	198	3	efficiency	efficiency	NN
10_1101-436634	198	4	of	of	IN
10_1101-436634	198	5	RegTools	RegTools	NNP
10_1101-436634	198	6	and	and	CC
10_1101-436634	198	7	increasing	increase	VBG
10_1101-436634	198	8	availability	availability	NN
10_1101-436634	198	9	and	and	CC
10_1101-436634	198	10	size	size	NN
10_1101-436634	198	11	of	of	IN
10_1101-436634	198	12	such	such	JJ
10_1101-436634	198	13	datasets	dataset	NNS
10_1101-436634	198	14	may	may	MD
10_1101-436634	198	15	also	also	RB
10_1101-436634	198	16	allow	allow	VB
10_1101-436634	198	17	for	for	IN
10_1101-436634	198	18	improved	improved	JJ
10_1101-436634	198	19	understanding	understanding	NN
10_1101-436634	198	20	of	of	IN
10_1101-436634	198	21	splice	splice	NN
10_1101-436634	198	22	regulatory	regulatory	JJ
10_1101-436634	198	23	motifs	motif	NNS
10_1101-436634	198	24	that	that	WDT
10_1101-436634	198	25	have	have	VBP
10_1101-436634	198	26	proven	prove	VBN
10_1101-436634	198	27	difficult	difficult	JJ
10_1101-436634	198	28	to	to	TO
10_1101-436634	198	29	accurately	accurately	RB
10_1101-436634	198	30	define	define	VB
10_1101-436634	198	31	such	such	JJ
10_1101-436634	198	32	as	as	IN
10_1101-436634	198	33	exonic	exonic	JJ
10_1101-436634	198	34	and	and	CC
10_1101-436634	198	35	intronic	intronic	JJ
10_1101-436634	198	36	splicing	splicing	NN
10_1101-436634	198	37	enhancers	enhancer	NNS
10_1101-436634	198	38	and	and	CC
10_1101-436634	198	39	silencers	silencer	NNS
10_1101-436634	198	40	.	.	.
10_1101-436634	199	1	Any	any	DT
10_1101-436634	199	2	group	group	NN
10_1101-436634	199	3	with	with	IN
10_1101-436634	199	4	paired	pair	VBN
10_1101-436634	199	5	DNA	DNA	NNP
10_1101-436634	199	6	and	and	CC
10_1101-436634	199	7	RNA	RNA	NNP
10_1101-436634	199	8	-	-	HYPH
10_1101-436634	199	9	seq	seq	NN
10_1101-436634	199	10	data	datum	NNS
10_1101-436634	199	11	for	for	IN
10_1101-436634	199	12	the	the	DT
10_1101-436634	199	13	same	same	JJ
10_1101-436634	199	14	samples	sample	NNS
10_1101-436634	199	15	stands	stand	VBZ
10_1101-436634	199	16	to	to	TO
10_1101-436634	199	17	benefit	benefit	VB
10_1101-436634	199	18	from	from	IN
10_1101-436634	199	19	the	the	DT
10_1101-436634	199	20	functionality	functionality	NN
10_1101-436634	199	21	of	of	IN
10_1101-436634	199	22	RegTools	RegTools	NNP
10_1101-436634	199	23	.	.	.
10_1101-436634	200	1	Methods	method	NNS
10_1101-436634	200	2	Software	software	NN
10_1101-436634	200	3	implementation	implementation	NN
10_1101-436634	200	4	RegTools	RegTools	NNP
10_1101-436634	200	5	is	be	VBZ
10_1101-436634	200	6	written	write	VBN
10_1101-436634	200	7	in	in	IN
10_1101-436634	200	8	C++	C++	NNP
10_1101-436634	200	9	.	.	.
10_1101-436634	201	1	CMake	CMake	NNP
10_1101-436634	201	2	is	be	VBZ
10_1101-436634	201	3	used	use	VBN
10_1101-436634	201	4	to	to	TO
10_1101-436634	201	5	build	build	VB
10_1101-436634	201	6	the	the	DT
10_1101-436634	201	7	executable	executable	JJ
10_1101-436634	201	8	from	from	IN
10_1101-436634	201	9	source	source	NN
10_1101-436634	201	10	code	code	NN
10_1101-436634	201	11	.	.	.
10_1101-436634	202	1	We	-PRON-	PRP
10_1101-436634	202	2	have	have	VBP
10_1101-436634	202	3	designed	design	VBN
10_1101-436634	202	4	the	the	DT
10_1101-436634	202	5	RegTools	RegTools	NNP
10_1101-436634	202	6	package	package	NN
10_1101-436634	202	7	to	to	TO
10_1101-436634	202	8	be	be	VB
10_1101-436634	202	9	self	self	NN
10_1101-436634	202	10	-	-	HYPH
10_1101-436634	202	11	contained	contain	VBN
10_1101-436634	202	12	in	in	IN
10_1101-436634	202	13	order	order	NN
10_1101-436634	202	14	to	to	TO
10_1101-436634	202	15	minimize	minimize	VB
10_1101-436634	202	16	external	external	JJ
10_1101-436634	202	17	software	software	NN
10_1101-436634	202	18	dependencies	dependency	NNS
10_1101-436634	202	19	.	.	.
10_1101-436634	203	1	A	a	DT
10_1101-436634	203	2	Unix	Unix	NNP
10_1101-436634	203	3	platform	platform	NN
10_1101-436634	203	4	with	with	IN
10_1101-436634	203	5	a	a	DT
10_1101-436634	203	6	C++	C++	NNP
10_1101-436634	203	7	compiler	compiler	NN
10_1101-436634	203	8	and	and	CC
10_1101-436634	203	9	CMake	cmake	NN
10_1101-436634	203	10	is	be	VBZ
10_1101-436634	203	11	the	the	DT
10_1101-436634	203	12	minimum	minimum	JJ
10_1101-436634	203	13	prerequisite	prerequisite	NN
10_1101-436634	203	14	for	for	IN
10_1101-436634	203	15	installing	instal	VBG
10_1101-436634	203	16	RegTools	regtool	NNS
10_1101-436634	203	17	.	.	.
10_1101-436634	204	1	Documentation	documentation	NN
10_1101-436634	204	2	for	for	IN
10_1101-436634	204	3	RegTools	RegTools	NNP
10_1101-436634	204	4	is	be	VBZ
10_1101-436634	204	5	maintained	maintain	VBN
10_1101-436634	204	6	as	as	IN
10_1101-436634	204	7	text	text	NN
10_1101-436634	204	8	files	file	NNS
10_1101-436634	204	9	within	within	IN
10_1101-436634	204	10	the	the	DT
10_1101-436634	204	11	source	source	NN
10_1101-436634	204	12	repository	repository	NN
10_1101-436634	204	13	to	to	TO
10_1101-436634	204	14	minimize	minimize	VB
10_1101-436634	204	15	divergence	divergence	NN
10_1101-436634	204	16	from	from	IN
10_1101-436634	204	17	the	the	DT
10_1101-436634	204	18	code	code	NN
10_1101-436634	204	19	.	.	.
10_1101-436634	205	1	We	-PRON-	PRP
10_1101-436634	205	2	have	have	VBP
10_1101-436634	205	3	implemented	implement	VBN
10_1101-436634	205	4	common	common	JJ
10_1101-436634	205	5	file	file	NN
10_1101-436634	205	6	handling	handle	VBG
10_1101-436634	205	7	tasks	task	NNS
10_1101-436634	205	8	in	in	IN
10_1101-436634	205	9	RegTools	RegTools	NNP
10_1101-436634	205	10	with	with	IN
10_1101-436634	205	11	the	the	DT
10_1101-436634	205	12	help	help	NN
10_1101-436634	205	13	of	of	IN
10_1101-436634	205	14	open	open	JJ
10_1101-436634	205	15	-	-	HYPH
10_1101-436634	205	16	source	source	NN
10_1101-436634	205	17	code	code	NN
10_1101-436634	205	18	from	from	IN
10_1101-436634	205	19	Samtools	Samtools	NNP
10_1101-436634	205	20	/	/	SYM
10_1101-436634	205	21	HTSlib26	HTSlib26	NNP
10_1101-436634	205	22	and	and	CC
10_1101-436634	205	23	BEDTools45	bedtools45	VB
10_1101-436634	205	24	in	in	IN
10_1101-436634	205	25	an	an	DT
10_1101-436634	205	26	effort	effort	NN
10_1101-436634	205	27	to	to	TO
10_1101-436634	205	28	ensure	ensure	VB
10_1101-436634	205	29	fast	fast	JJ
10_1101-436634	205	30	performance	performance	NN
10_1101-436634	205	31	,	,	,
10_1101-436634	205	32	consistent	consistent	JJ
10_1101-436634	205	33	file	file	NN
10_1101-436634	205	34	handling	handling	NN
10_1101-436634	205	35	,	,	,
10_1101-436634	205	36	and	and	CC
10_1101-436634	205	37	interoperability	interoperability	NN
10_1101-436634	205	38	with	with	IN
10_1101-436634	205	39	any	any	DT
10_1101-436634	205	40	aligner	aligner	NN
10_1101-436634	205	41	that	that	WDT
10_1101-436634	205	42	adheres	adhere	VBZ
10_1101-436634	205	43	to	to	IN
10_1101-436634	205	44	the	the	DT
10_1101-436634	205	45	BAM	BAM	NNP
10_1101-436634	205	46	specification	specification	NN
10_1101-436634	205	47	.	.	.
10_1101-436634	206	1	Statistical	statistical	JJ
10_1101-436634	206	2	tests	test	NNS
10_1101-436634	206	3	are	be	VBP
10_1101-436634	206	4	conducted	conduct	VBN
10_1101-436634	206	5	within	within	IN
10_1101-436634	206	6	RegTools	RegTools	NNP
10_1101-436634	206	7	using	use	VBG
10_1101-436634	206	8	the	the	DT
10_1101-436634	206	9	RMath	RMath	NNP
10_1101-436634	206	10	framework	framework	NN
10_1101-436634	206	11	.	.	.
10_1101-436634	207	1	Travis	Travis	NNP
10_1101-436634	207	2	CI	CI	NNP
10_1101-436634	207	3	and	and	CC
10_1101-436634	207	4	Coveralls	Coveralls	NNP
10_1101-436634	207	5	are	be	VBP
10_1101-436634	207	6	used	use	VBN
10_1101-436634	207	7	to	to	TO
10_1101-436634	207	8	automate	automate	VB
10_1101-436634	207	9	and	and	CC
10_1101-436634	207	10	monitor	monitor	VB
10_1101-436634	207	11	software	software	NN
10_1101-436634	207	12	compilation	compilation	NN
10_1101-436634	207	13	and	and	CC
10_1101-436634	207	14	unit	unit	NN
10_1101-436634	207	15	tests	test	NNS
10_1101-436634	207	16	to	to	TO
10_1101-436634	207	17	ensure	ensure	VB
10_1101-436634	207	18	software	software	NN
10_1101-436634	207	19	functionality	functionality	NN
10_1101-436634	207	20	.	.	.
10_1101-436634	208	1	We	-PRON-	PRP
10_1101-436634	208	2	utilized	utilize	VBD
10_1101-436634	208	3	the	the	DT
10_1101-436634	208	4	Google	Google	NNP
10_1101-436634	208	5	Test	Test	NNP
10_1101-436634	208	6	framework	framework	NN
10_1101-436634	208	7	to	to	TO
10_1101-436634	208	8	write	write	VB
10_1101-436634	208	9	unit	unit	NN
10_1101-436634	208	10	tests	test	NNS
10_1101-436634	208	11	.	.	.
10_1101-436634	209	1	RegTools	RegTools	NNP
10_1101-436634	209	2	consists	consist	VBZ
10_1101-436634	209	3	of	of	IN
10_1101-436634	209	4	a	a	DT
10_1101-436634	209	5	core	core	NN
10_1101-436634	209	6	set	set	NN
10_1101-436634	209	7	of	of	IN
10_1101-436634	209	8	modules	module	NNS
10_1101-436634	209	9	for	for	IN
10_1101-436634	209	10	variant	variant	JJ
10_1101-436634	209	11	annotation	annotation	NN
10_1101-436634	209	12	,	,	,
10_1101-436634	209	13	junction	junction	NN
10_1101-436634	209	14	extraction	extraction	NN
10_1101-436634	209	15	,	,	,
10_1101-436634	209	16	junction	junction	NN
10_1101-436634	209	17	annotation	annotation	NN
10_1101-436634	209	18	,	,	,
10_1101-436634	209	19	and	and	CC
10_1101-436634	209	20	GTF	GTF	NNP
10_1101-436634	209	21	utilities	utility	NNS
10_1101-436634	209	22	.	.	.
10_1101-436634	210	1	Higher	high	JJR
10_1101-436634	210	2	level	level	NN
10_1101-436634	210	3	modules	module	NNS
10_1101-436634	210	4	such	such	JJ
10_1101-436634	210	5	as	as	IN
10_1101-436634	210	6	cis	cis	NN
10_1101-436634	210	7	-	-	HYPH
10_1101-436634	210	8	splice	splice	NN
10_1101-436634	210	9	-	-	HYPH
10_1101-436634	210	10	effects	effect	NNS
10_1101-436634	210	11	make	make	VBP
10_1101-436634	210	12	use	use	NN
10_1101-436634	210	13	of	of	IN
10_1101-436634	210	14	the	the	DT
10_1101-436634	210	15	lower	low	JJR
10_1101-436634	210	16	level	level	NN
10_1101-436634	210	17	modules	module	NNS
10_1101-436634	210	18	to	to	TO
10_1101-436634	210	19	perform	perform	VB
10_1101-436634	210	20	more	more	RBR
10_1101-436634	210	21	complex	complex	JJ
10_1101-436634	210	22	analyses	analysis	NNS
10_1101-436634	210	23	.	.	.
10_1101-436634	211	1	We	-PRON-	PRP
10_1101-436634	211	2	hope	hope	VBP
10_1101-436634	211	3	that	that	IN
10_1101-436634	211	4	bioinformaticians	bioinformatician	NNS
10_1101-436634	211	5	familiar	familiar	JJ
10_1101-436634	211	6	with	with	IN
10_1101-436634	211	7	C	C	NNP
10_1101-436634	211	8	/	/	SYM
10_1101-436634	211	9	C++	C++	NNP
10_1101-436634	211	10	can	can	MD
10_1101-436634	211	11	re	re	VB
10_1101-436634	211	12	-	-	VB
10_1101-436634	211	13	use	use	VB
10_1101-436634	211	14	or	or	CC
10_1101-436634	211	15	adapt	adapt	VB
10_1101-436634	211	16	the	the	DT
10_1101-436634	211	17	RegTools	RegTools	NNP
10_1101-436634	211	18	code	code	NN
10_1101-436634	211	19	to	to	TO
10_1101-436634	211	20	implement	implement	VB
10_1101-436634	211	21	similar	similar	JJ
10_1101-436634	211	22	tasks	task	NNS
10_1101-436634	211	23	.	.	.
10_1101-436634	212	1	Benchmarking	benchmarke	VBG
10_1101-436634	212	2	Performance	Performance	NNP
10_1101-436634	212	3	metrics	metric	NNS
10_1101-436634	212	4	were	be	VBD
10_1101-436634	212	5	calculated	calculate	VBN
10_1101-436634	212	6	for	for	IN
10_1101-436634	212	7	all	all	DT
10_1101-436634	212	8	RegTools	RegTools	NNP
10_1101-436634	212	9	commands	command	NNS
10_1101-436634	212	10	.	.	.
10_1101-436634	213	1	Each	each	DT
10_1101-436634	213	2	command	command	NN
10_1101-436634	213	3	was	be	VBD
10_1101-436634	213	4	run	run	VBN
10_1101-436634	213	5	with	with	IN
10_1101-436634	213	6	default	default	NN
10_1101-436634	213	7	parameters	parameter	NNS
10_1101-436634	213	8	on	on	IN
10_1101-436634	213	9	a	a	DT
10_1101-436634	213	10	single	single	JJ
10_1101-436634	213	11	blade	blade	NN
10_1101-436634	213	12	server	server	NN
10_1101-436634	213	13	(	(	-LRB-
10_1101-436634	213	14	Intel(R	intel(r	NN
10_1101-436634	213	15	)	)	-RRB-
10_1101-436634	213	16	Xeon(R	Xeon(R	NNP
10_1101-436634	213	17	)	)	-RRB-
10_1101-436634	213	18	CPU	CPU	NNP
10_1101-436634	213	19	E5	E5	NNP
10_1101-436634	213	20	-	-	HYPH
10_1101-436634	213	21	2660	2660	CD
10_1101-436634	213	22	v2	v2	NN
10_1101-436634	213	23	@	@	CC
10_1101-436634	213	24	2.20GHz	2.20ghz	NN
10_1101-436634	213	25	)	)	-RRB-
10_1101-436634	213	26	with	with	IN
10_1101-436634	213	27	10	10	CD
10_1101-436634	213	28	GB	GB	NNS
10_1101-436634	213	29	of	of	IN
10_1101-436634	213	30	RAM	ram	NN
10_1101-436634	213	31	and	and	CC
10_1101-436634	213	32	10	10	CD
10_1101-436634	213	33	replicates	replicate	NNS
10_1101-436634	213	34	for	for	IN
10_1101-436634	213	35	each	each	DT
10_1101-436634	213	36	data	data	NN
10_1101-436634	213	37	point	point	NN
10_1101-436634	213	38	(	(	-LRB-
10_1101-436634	213	39	Supplementary	Supplementary	NNP
10_1101-436634	213	40	Figure	Figure	NNP
10_1101-436634	213	41	1	1	CD
10_1101-436634	213	42	)	)	-RRB-
10_1101-436634	213	43	.	.	.
10_1101-436634	214	1	Specifically	specifically	RB
10_1101-436634	214	2	for	for	IN
10_1101-436634	214	3	cis	cis	NN
10_1101-436634	214	4	-	-	HYPH
10_1101-436634	214	5	splice	splice	NN
10_1101-436634	214	6	-	-	HYPH
10_1101-436634	214	7	effects	effect	NNS
10_1101-436634	214	8	identify	identify	VBP
10_1101-436634	214	9	,	,	,
10_1101-436634	214	10	we	-PRON-	PRP
10_1101-436634	214	11	started	start	VBD
10_1101-436634	214	12	with	with	IN
10_1101-436634	214	13	random	random	JJ
10_1101-436634	214	14	selections	selection	NNS
10_1101-436634	214	15	of	of	IN
10_1101-436634	214	16	somatic	somatic	JJ
10_1101-436634	214	17	variants	variant	NNS
10_1101-436634	214	18	,	,	,
10_1101-436634	214	19	ranging	range	VBG
10_1101-436634	214	20	from	from	IN
10_1101-436634	214	21	10,000	10,000	CD
10_1101-436634	214	22	-	-	SYM
10_1101-436634	214	23	1,500,000	1,500,000	CD
10_1101-436634	214	24	,	,	,
10_1101-436634	214	25	across	across	IN
10_1101-436634	214	26	8	8	CD
10_1101-436634	214	27	data	data	NN
10_1101-436634	214	28	subsets	subset	NNS
10_1101-436634	214	29	.	.	.
10_1101-436634	215	1	Using	use	VBG
10_1101-436634	215	2	the	the	DT
10_1101-436634	215	3	output	output	NN
10_1101-436634	215	4	from	from	IN
10_1101-436634	215	5	cis	cis	NN
10_1101-436634	215	6	-	-	HYPH
10_1101-436634	215	7	splice	splice	NN
10_1101-436634	215	8	-	-	HYPH
10_1101-436634	215	9	effects	effect	NNS
10_1101-436634	215	10	identify	identify	VBP
10_1101-436634	215	11	,	,	,
10_1101-436634	215	12	variants	variant	NNS
10_1101-436634	215	13	annotate	annotate	JJ
10_1101-436634	215	14	was	be	VBD
10_1101-436634	215	15	run	run	VBN
10_1101-436634	215	16	on	on	IN
10_1101-436634	215	17	somatic	somatic	JJ
10_1101-436634	215	18	variants	variant	NNS
10_1101-436634	215	19	from	from	IN
10_1101-436634	215	20	the	the	DT
10_1101-436634	215	21	8	8	CD
10_1101-436634	215	22	subsets	subset	NNS
10_1101-436634	215	23	(	(	-LRB-
10_1101-436634	215	24	range	range	NN
10_1101-436634	215	25	:	:	:
10_1101-436634	215	26	0	0	CD
10_1101-436634	215	27	-	-	SYM
10_1101-436634	215	28	17,742	17,742	CD
10_1101-436634	215	29	)	)	-RRB-
10_1101-436634	215	30	predicted	predict	VBD
10_1101-436634	215	31	to	to	TO
10_1101-436634	215	32	have	have	VB
10_1101-436634	215	33	a	a	DT
10_1101-436634	215	34	splicing	splicing	NN
10_1101-436634	215	35	consequence	consequence	NN
10_1101-436634	215	36	.	.	.
10_1101-436634	216	1	The	the	DT
10_1101-436634	216	2	function	function	NN
10_1101-436634	216	3	junctions	junction	NNS
10_1101-436634	216	4	extract	extract	NN
10_1101-436634	216	5	was	be	VBD
10_1101-436634	216	6	performed	perform	VBN
10_1101-436634	216	7	on	on	IN
10_1101-436634	216	8	the	the	DT
10_1101-436634	216	9	HCC1395	HCC1395	NNP
10_1101-436634	216	10	tumor	tumor	NN
10_1101-436634	216	11	RNA	RNA	NNP
10_1101-436634	216	12	-	-	HYPH
10_1101-436634	216	13	seq	seq	NN
10_1101-436634	216	14	data	datum	NNS
10_1101-436634	216	15	aligned	align	VBN
10_1101-436634	216	16	with	with	IN
10_1101-436634	216	17	HISAT	HISAT	NNP
10_1101-436634	216	18	to	to	IN
10_1101-436634	216	19	GRCh37	GRCh37	NNP
10_1101-436634	216	20	and	and	CC
10_1101-436634	216	21	randomly	randomly	RB
10_1101-436634	216	22	downsampled	downsample	VBN
10_1101-436634	216	23	at	at	IN
10_1101-436634	216	24	intervals	interval	NNS
10_1101-436634	216	25	ranging	range	VBG
10_1101-436634	216	26	from	from	IN
10_1101-436634	216	27	10	10	CD
10_1101-436634	216	28	-	-	SYM
10_1101-436634	216	29	100	100	CD
10_1101-436634	216	30	%	%	NN
10_1101-436634	216	31	.	.	.
10_1101-436634	217	1	Using	use	VBG
10_1101-436634	217	2	output	output	NN
10_1101-436634	217	3	from	from	IN
10_1101-436634	217	4	junctions	junction	NNS
10_1101-436634	217	5	extract	extract	NN
10_1101-436634	217	6	,	,	,
10_1101-436634	217	7	junctions	junction	NNS
10_1101-436634	217	8	annotate	annotate	NN
10_1101-436634	217	9	was	be	VBD
10_1101-436634	217	10	performed	perform	VBN
10_1101-436634	217	11	for	for	IN
10_1101-436634	217	12	7	7	CD
10_1101-436634	217	13	data	datum	NNS
10_1101-436634	217	14	subsets	subset	NNS
10_1101-436634	217	15	ranging	range	VBG
10_1101-436634	217	16	from	from	IN
10_1101-436634	217	17	1,000	1,000	CD
10_1101-436634	217	18	-	-	SYM
10_1101-436634	217	19	500,000	500,000	CD
10_1101-436634	217	20	randomly	randomly	RB
10_1101-436634	217	21	selected	select	VBN
10_1101-436634	217	22	junctions	junction	NNS
10_1101-436634	217	23	.	.	.
10_1101-436634	218	1	.CC	.CC	NFP
10_1101-436634	218	2	-	-	:
10_1101-436634	218	3	BY	by	IN
10_1101-436634	218	4	-	-	HYPH
10_1101-436634	218	5	NC	NC	NNP
10_1101-436634	218	6	-	-	HYPH
10_1101-436634	218	7	ND	ND	NNP
10_1101-436634	218	8	4.0	4.0	CD
10_1101-436634	218	9	International	international	JJ
10_1101-436634	218	10	licensea	licensea	NNS
10_1101-436634	218	11	certified	certify	VBN
10_1101-436634	218	12	by	by	IN
10_1101-436634	218	13	peer	peer	NN
10_1101-436634	218	14	review	review	NN
10_1101-436634	218	15	)	)	-RRB-
10_1101-436634	218	16	is	be	VBZ
10_1101-436634	218	17	the	the	DT
10_1101-436634	218	18	author	author	NN
10_1101-436634	218	19	/	/	SYM
10_1101-436634	218	20	funder	funder	NN
10_1101-436634	218	21	,	,	,
10_1101-436634	218	22	who	who	WP
10_1101-436634	218	23	has	have	VBZ
10_1101-436634	218	24	granted	grant	VBN
10_1101-436634	218	25	bioRxiv	biorxiv	IN
10_1101-436634	218	26	a	a	DT
10_1101-436634	218	27	license	license	NN
10_1101-436634	218	28	to	to	TO
10_1101-436634	218	29	display	display	VB
10_1101-436634	218	30	the	the	DT
10_1101-436634	218	31	preprint	preprint	NN
10_1101-436634	218	32	in	in	IN
10_1101-436634	218	33	perpetuity	perpetuity	NN
10_1101-436634	218	34	.	.	.
10_1101-436634	219	1	It	-PRON-	PRP
10_1101-436634	219	2	is	be	VBZ
10_1101-436634	219	3	made	make	VBN
10_1101-436634	219	4	available	available	JJ
10_1101-436634	219	5	under	under	IN
10_1101-436634	219	6	The	the	DT
10_1101-436634	219	7	copyright	copyright	NN
10_1101-436634	219	8	holder	holder	NN
10_1101-436634	219	9	for	for	IN
10_1101-436634	219	10	this	this	DT
10_1101-436634	219	11	preprint	preprint	NN
10_1101-436634	219	12	(	(	-LRB-
10_1101-436634	219	13	which	which	WDT
10_1101-436634	219	14	was	be	VBD
10_1101-436634	219	15	notthis	notthis	DT
10_1101-436634	219	16	version	version	NN
10_1101-436634	219	17	posted	post	VBN
10_1101-436634	219	18	January	January	NNP
10_1101-436634	219	19	5	5	CD
10_1101-436634	219	20	,	,	,
10_1101-436634	219	21	2021	2021	CD
10_1101-436634	219	22	.	.	.
10_1101-436634	219	23	;	;	:
10_1101-436634	219	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	219	25	:	:	:
10_1101-436634	219	26	bioRxiv	biorxiv	VB
10_1101-436634	219	27	preprint	preprint	NN
10_1101-436634	219	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	219	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	CD
10_1101-436634	219	30	11	11	CD
10_1101-436634	219	31	Benchmark	Benchmark	NNP
10_1101-436634	219	32	tests	test	NNS
10_1101-436634	219	33	revealed	reveal	VBD
10_1101-436634	219	34	an	an	DT
10_1101-436634	219	35	approximately	approximately	RB
10_1101-436634	219	36	linear	linear	JJ
10_1101-436634	219	37	performance	performance	NN
10_1101-436634	219	38	for	for	IN
10_1101-436634	219	39	all	all	DT
10_1101-436634	219	40	functions	function	NNS
10_1101-436634	219	41	.	.	.
10_1101-436634	220	1	Variance	variance	NN
10_1101-436634	220	2	between	between	IN
10_1101-436634	220	3	real	real	JJ
10_1101-436634	220	4	and	and	CC
10_1101-436634	220	5	CPU	cpu	NN
10_1101-436634	220	6	time	time	NN
10_1101-436634	220	7	is	be	VBZ
10_1101-436634	220	8	highly	highly	RB
10_1101-436634	220	9	dependent	dependent	JJ
10_1101-436634	220	10	on	on	IN
10_1101-436634	220	11	the	the	DT
10_1101-436634	220	12	I	i	NN
10_1101-436634	220	13	/	/	SYM
10_1101-436634	220	14	O	o	UH
10_1101-436634	220	15	speed	speed	NN
10_1101-436634	220	16	of	of	IN
10_1101-436634	220	17	the	the	DT
10_1101-436634	220	18	write	write	JJ
10_1101-436634	220	19	-	-	HYPH
10_1101-436634	220	20	disk	disk	NN
10_1101-436634	220	21	and	and	CC
10_1101-436634	220	22	could	could	MD
10_1101-436634	220	23	account	account	VB
10_1101-436634	220	24	for	for	IN
10_1101-436634	220	25	artificially	artificially	RB
10_1101-436634	220	26	inflated	inflate	VBN
10_1101-436634	220	27	real	real	JJ
10_1101-436634	220	28	time	time	NN
10_1101-436634	220	29	values	value	NNS
10_1101-436634	220	30	given	give	VBN
10_1101-436634	220	31	multiple	multiple	JJ
10_1101-436634	220	32	jobs	job	NNS
10_1101-436634	220	33	writing	write	VBG
10_1101-436634	220	34	to	to	IN
10_1101-436634	220	35	the	the	DT
10_1101-436634	220	36	same	same	JJ
10_1101-436634	220	37	disk	disk	NN
10_1101-436634	220	38	at	at	IN
10_1101-436634	220	39	once	once	RB
10_1101-436634	220	40	.	.	.
10_1101-436634	221	1	The	the	DT
10_1101-436634	221	2	most	most	RBS
10_1101-436634	221	3	computationally	computationally	RB
10_1101-436634	221	4	expensive	expensive	JJ
10_1101-436634	221	5	function	function	NN
10_1101-436634	221	6	in	in	IN
10_1101-436634	221	7	a	a	DT
10_1101-436634	221	8	typical	typical	JJ
10_1101-436634	221	9	analysis	analysis	NN
10_1101-436634	221	10	workflow	workflow	NN
10_1101-436634	221	11	was	be	VBD
10_1101-436634	221	12	junctions	junction	NNS
10_1101-436634	221	13	extract	extract	NNP
10_1101-436634	221	14	,	,	,
10_1101-436634	221	15	which	which	WDT
10_1101-436634	221	16	on	on	IN
10_1101-436634	221	17	average	average	JJ
10_1101-436634	221	18	processed	process	VBD
10_1101-436634	221	19	33,091	33,091	CD
10_1101-436634	221	20	reads	read	NNS
10_1101-436634	221	21	/	/	SYM
10_1101-436634	221	22	second	second	NN
10_1101-436634	221	23	(	(	-LRB-
10_1101-436634	221	24	CPU	cpu	NN
10_1101-436634	221	25	)	)	-RRB-
10_1101-436634	221	26	and	and	CC
10_1101-436634	221	27	took	take	VBD
10_1101-436634	221	28	an	an	DT
10_1101-436634	221	29	average	average	NN
10_1101-436634	221	30	of	of	IN
10_1101-436634	221	31	43.4	43.4	CD
10_1101-436634	221	32	real	real	JJ
10_1101-436634	221	33	vs	vs	IN
10_1101-436634	221	34	41.7	41.7	CD
10_1101-436634	221	35	CPU	cpu	NN
10_1101-436634	221	36	minutes	minute	NNS
10_1101-436634	221	37	to	to	TO
10_1101-436634	221	38	run	run	VB
10_1101-436634	221	39	on	on	IN
10_1101-436634	221	40	a	a	DT
10_1101-436634	221	41	full	full	JJ
10_1101-436634	221	42	bam	bam	NN
10_1101-436634	221	43	file	file	NN
10_1101-436634	221	44	(	(	-LRB-
10_1101-436634	221	45	82,807,868	82,807,868	CD
10_1101-436634	221	46	reads	read	NNS
10_1101-436634	221	47	total	total	NN
10_1101-436634	221	48	)	)	-RRB-
10_1101-436634	221	49	.	.	.
10_1101-436634	222	1	The	the	DT
10_1101-436634	222	2	function	function	NN
10_1101-436634	222	3	junctions	junction	NNS
10_1101-436634	222	4	annotate	annotate	NN
10_1101-436634	222	5	was	be	VBD
10_1101-436634	222	6	the	the	DT
10_1101-436634	222	7	next	next	JJ
10_1101-436634	222	8	most	most	RBS
10_1101-436634	222	9	computationally	computationally	RB
10_1101-436634	222	10	intensive	intensive	JJ
10_1101-436634	222	11	function	function	NN
10_1101-436634	222	12	and	and	CC
10_1101-436634	222	13	took	take	VBD
10_1101-436634	222	14	an	an	DT
10_1101-436634	222	15	average	average	NN
10_1101-436634	222	16	of	of	IN
10_1101-436634	222	17	33.0	33.0	CD
10_1101-436634	222	18	real/8.55	real/8.55	JJ
10_1101-436634	222	19	CPU	cpu	NN
10_1101-436634	222	20	minutes	minute	NNS
10_1101-436634	222	21	to	to	TO
10_1101-436634	222	22	run	run	VB
10_1101-436634	222	23	on	on	IN
10_1101-436634	222	24	500,000	500,000	CD
10_1101-436634	222	25	junctions	junction	NNS
10_1101-436634	222	26	,	,	,
10_1101-436634	222	27	processing	process	VBG
10_1101-436634	222	28	975	975	CD
10_1101-436634	222	29	junctions	junction	NNS
10_1101-436634	222	30	/	/	SYM
10_1101-436634	222	31	second	second	JJ
10_1101-436634	222	32	(	(	-LRB-
10_1101-436634	222	33	CPU	cpu	NN
10_1101-436634	222	34	)	)	-RRB-
10_1101-436634	222	35	.	.	.
10_1101-436634	223	1	The	the	DT
10_1101-436634	223	2	other	other	JJ
10_1101-436634	223	3	functions	function	NNS
10_1101-436634	223	4	were	be	VBD
10_1101-436634	223	5	comparatively	comparatively	RB
10_1101-436634	223	6	faster	fast	JJR
10_1101-436634	223	7	with	with	IN
10_1101-436634	223	8	cis	cis	NN
10_1101-436634	223	9	-	-	HYPH
10_1101-436634	223	10	splice	splice	NN
10_1101-436634	223	11	-	-	HYPH
10_1101-436634	223	12	effects	effect	NNS
10_1101-436634	223	13	identify	identify	VBP
10_1101-436634	223	14	and	and	CC
10_1101-436634	223	15	variants	variant	NNS
10_1101-436634	223	16	annotate	annotate	VBP
10_1101-436634	223	17	able	able	JJ
10_1101-436634	223	18	to	to	TO
10_1101-436634	223	19	process	process	VB
10_1101-436634	223	20	3,105	3,105	CD
10_1101-436634	223	21	and	and	CC
10_1101-436634	223	22	118	118	CD
10_1101-436634	223	23	variants	variant	NNS
10_1101-436634	223	24	per	per	IN
10_1101-436634	223	25	second	second	NN
10_1101-436634	223	26	(	(	-LRB-
10_1101-436634	223	27	CPU	cpu	NN
10_1101-436634	223	28	)	)	-RRB-
10_1101-436634	223	29	,	,	,
10_1101-436634	223	30	respectively	respectively	RB
10_1101-436634	223	31	.	.	.
10_1101-436634	224	1	To	to	TO
10_1101-436634	224	2	process	process	VB
10_1101-436634	224	3	a	a	DT
10_1101-436634	224	4	typical	typical	JJ
10_1101-436634	224	5	candidate	candidate	NN
10_1101-436634	224	6	variant	variant	JJ
10_1101-436634	224	7	list	list	NN
10_1101-436634	224	8	of	of	IN
10_1101-436634	224	9	1,500,000	1,500,000	CD
10_1101-436634	224	10	variants	variant	NNS
10_1101-436634	224	11	and	and	CC
10_1101-436634	224	12	a	a	DT
10_1101-436634	224	13	corresponding	corresponding	JJ
10_1101-436634	224	14	RNA	RNA	NNP
10_1101-436634	224	15	-	-	HYPH
10_1101-436634	224	16	seq	seq	NN
10_1101-436634	224	17	BAM	BAM	NNP
10_1101-436634	224	18	file	file	NN
10_1101-436634	224	19	of	of	IN
10_1101-436634	224	20	82,807,868	82,807,868	CD
10_1101-436634	224	21	reads	read	NNS
10_1101-436634	224	22	with	with	IN
10_1101-436634	224	23	cis	cis	NN
10_1101-436634	224	24	-	-	HYPH
10_1101-436634	224	25	splice	splice	NN
10_1101-436634	224	26	-	-	HYPH
10_1101-436634	224	27	effects	effect	NNS
10_1101-436634	224	28	identify	identify	VBP
10_1101-436634	224	29	takes	take	VBZ
10_1101-436634	224	30	~	~	NFP
10_1101-436634	224	31	8.20	8.20	CD
10_1101-436634	224	32	real/8.05	real/8.05	JJ
10_1101-436634	224	33	CPU	cpu	NN
10_1101-436634	224	34	minutes	minute	NNS
10_1101-436634	224	35	(	(	-LRB-
10_1101-436634	224	36	Supplementary	Supplementary	NNP
10_1101-436634	224	37	Figure	Figure	NNP
10_1101-436634	224	38	1	1	CD
10_1101-436634	224	39	)	)	-RRB-
10_1101-436634	224	40	.	.	.
10_1101-436634	225	1	Performance	performance	NN
10_1101-436634	225	2	metrics	metric	NNS
10_1101-436634	225	3	were	be	VBD
10_1101-436634	225	4	also	also	RB
10_1101-436634	225	5	calculated	calculate	VBN
10_1101-436634	225	6	for	for	IN
10_1101-436634	225	7	the	the	DT
10_1101-436634	225	8	statistics	statistic	NNS
10_1101-436634	225	9	script	script	NN
10_1101-436634	225	10	and	and	CC
10_1101-436634	225	11	its	-PRON-	PRP$
10_1101-436634	225	12	associated	associated	NNP
10_1101-436634	225	13	wrapper	wrapper	NNP
10_1101-436634	225	14	script	script	NN
10_1101-436634	225	15	that	that	WDT
10_1101-436634	225	16	handles	handle	NNS
10_1101-436634	225	17	dividing	divide	VBG
10_1101-436634	225	18	the	the	DT
10_1101-436634	225	19	variants	variant	NNS
10_1101-436634	225	20	into	into	IN
10_1101-436634	225	21	smaller	small	JJR
10_1101-436634	225	22	chunks	chunk	NNS
10_1101-436634	225	23	for	for	IN
10_1101-436634	225	24	processing	processing	NN
10_1101-436634	225	25	to	to	TO
10_1101-436634	225	26	limit	limit	VB
10_1101-436634	225	27	RAM	ram	NN
10_1101-436634	225	28	usage	usage	NN
10_1101-436634	225	29	.	.	.
10_1101-436634	226	1	This	this	DT
10_1101-436634	226	2	command	command	NN
10_1101-436634	226	3	,	,	,
10_1101-436634	226	4	compare_junctions	compare_junction	NNS
10_1101-436634	226	5	,	,	,
10_1101-436634	226	6	was	be	VBD
10_1101-436634	226	7	benchmarked	benchmarke	VBN
10_1101-436634	226	8	in	in	IN
10_1101-436634	226	9	January	January	NNP
10_1101-436634	226	10	2020	2020	CD
10_1101-436634	226	11	using	use	VBG
10_1101-436634	226	12	Amazon	Amazon	NNP
10_1101-436634	226	13	Web	Web	NNP
10_1101-436634	226	14	Services	Services	NNPS
10_1101-436634	226	15	(	(	-LRB-
10_1101-436634	226	16	AWS	AWS	NNP
10_1101-436634	226	17	)	)	-RRB-
10_1101-436634	226	18	on	on	IN
10_1101-436634	226	19	a	a	DT
10_1101-436634	226	20	m5.4xlarge	m5.4xlarge	NNP
10_1101-436634	226	21	instance	instance	NN
10_1101-436634	226	22	,	,	,
10_1101-436634	226	23	based	base	VBN
10_1101-436634	226	24	on	on	IN
10_1101-436634	226	25	the	the	DT
10_1101-436634	226	26	Amazon	Amazon	NNP
10_1101-436634	226	27	Linux	Linux	NNP
10_1101-436634	226	28	2	2	CD
10_1101-436634	226	29	AMI	AMI	NNP
10_1101-436634	226	30	,	,	,
10_1101-436634	226	31	with	with	IN
10_1101-436634	226	32	64	64	CD
10_1101-436634	226	33	Gb	Gb	NNS
10_1101-436634	226	34	of	of	IN
10_1101-436634	226	35	RAM	ram	NN
10_1101-436634	226	36	,	,	,
10_1101-436634	226	37	16	16	CD
10_1101-436634	226	38	vCPUs	vcpu	NNS
10_1101-436634	226	39	,	,	,
10_1101-436634	226	40	and	and	CC
10_1101-436634	226	41	a	a	DT
10_1101-436634	226	42	mounted	mount	VBN
10_1101-436634	226	43	1	1	CD
10_1101-436634	226	44	TB	TB	NNP
10_1101-436634	226	45	SSD	SSD	NNP
10_1101-436634	226	46	EBS	EBS	NNP
10_1101-436634	226	47	volume	volume	NN
10_1101-436634	226	48	with	with	IN
10_1101-436634	226	49	3000	3000	CD
10_1101-436634	226	50	IOPS	IOPS	NNP
10_1101-436634	226	51	.	.	.
10_1101-436634	227	1	These	these	DT
10_1101-436634	227	2	data	datum	NNS
10_1101-436634	227	3	were	be	VBD
10_1101-436634	227	4	generated	generate	VBN
10_1101-436634	227	5	from	from	IN
10_1101-436634	227	6	running	run	VBG
10_1101-436634	227	7	compare_junctions	compare_junction	NNS
10_1101-436634	227	8	on	on	IN
10_1101-436634	227	9	each	each	DT
10_1101-436634	227	10	of	of	IN
10_1101-436634	227	11	the	the	DT
10_1101-436634	227	12	included	included	JJ
10_1101-436634	227	13	cohorts	cohort	NNS
10_1101-436634	227	14	,	,	,
10_1101-436634	227	15	with	with	IN
10_1101-436634	227	16	the	the	DT
10_1101-436634	227	17	largest	large	JJS
10_1101-436634	227	18	being	be	VBG
10_1101-436634	227	19	our	-PRON-	PRP$
10_1101-436634	227	20	BRCA	BRCA	NNP
10_1101-436634	227	21	cohort	cohort	NN
10_1101-436634	227	22	(	(	-LRB-
10_1101-436634	227	23	1022	1022	CD
10_1101-436634	227	24	sample	sample	NN
10_1101-436634	227	25	)	)	-RRB-
10_1101-436634	227	26	which	which	WDT
10_1101-436634	227	27	processed	process	VBD
10_1101-436634	227	28	3.64	3.64	CD
10_1101-436634	227	29	events	event	NNS
10_1101-436634	227	30	per	per	IN
10_1101-436634	227	31	second	second	NN
10_1101-436634	227	32	(	(	-LRB-
10_1101-436634	227	33	CPU	cpu	NN
10_1101-436634	227	34	)	)	-RRB-
10_1101-436634	227	35	.	.	.
10_1101-436634	228	1	Using	use	VBG
10_1101-436634	228	2	RegTools	RegTools	NNP
10_1101-436634	228	3	to	to	TO
10_1101-436634	228	4	identify	identify	VB
10_1101-436634	228	5	cis	cis	NN
10_1101-436634	228	6	-	-	HYPH
10_1101-436634	228	7	acting	acting	NN
10_1101-436634	228	8	,	,	,
10_1101-436634	228	9	splice	splice	NN
10_1101-436634	228	10	altering	altering	NN
10_1101-436634	228	11	variants	variant	NNS
10_1101-436634	228	12	RegTools	RegTools	NNP
10_1101-436634	228	13	contains	contain	VBZ
10_1101-436634	228	14	three	three	CD
10_1101-436634	228	15	sub	sub	NN
10_1101-436634	228	16	-	-	HYPH
10_1101-436634	228	17	modules	module	NNS
10_1101-436634	228	18	:	:	:
10_1101-436634	228	19	“	"	``
10_1101-436634	228	20	variants	variant	NNS
10_1101-436634	228	21	”	"	''
10_1101-436634	228	22	,	,	,
10_1101-436634	228	23	“	"	``
10_1101-436634	228	24	junctions	junction	NNS
10_1101-436634	228	25	”	"	''
10_1101-436634	228	26	,	,	,
10_1101-436634	228	27	and	and	CC
10_1101-436634	228	28	“	"	``
10_1101-436634	228	29	cis	cis	NN
10_1101-436634	228	30	-	-	HYPH
10_1101-436634	228	31	splice	splice	NN
10_1101-436634	228	32	-	-	HYPH
10_1101-436634	228	33	effects	effect	NNS
10_1101-436634	228	34	”	"	''
10_1101-436634	228	35	.	.	.
10_1101-436634	229	1	For	for	IN
10_1101-436634	229	2	complete	complete	JJ
10_1101-436634	229	3	instructions	instruction	NNS
10_1101-436634	229	4	on	on	IN
10_1101-436634	229	5	usage	usage	NN
10_1101-436634	229	6	,	,	,
10_1101-436634	229	7	including	include	VBG
10_1101-436634	229	8	a	a	DT
10_1101-436634	229	9	detailed	detailed	JJ
10_1101-436634	229	10	workflow	workflow	NN
10_1101-436634	229	11	for	for	IN
10_1101-436634	229	12	how	how	WRB
10_1101-436634	229	13	to	to	TO
10_1101-436634	229	14	analyze	analyze	VB
10_1101-436634	229	15	cohorts	cohort	NNS
10_1101-436634	229	16	using	use	VBG
10_1101-436634	229	17	RegTools	RegTools	NNP
10_1101-436634	229	18	,	,	,
10_1101-436634	229	19	please	please	UH
10_1101-436634	229	20	visit	visit	VB
10_1101-436634	229	21	regtools.org	regtools.org	ADD
10_1101-436634	229	22	.	.	.
10_1101-436634	230	1	Variants	variant	NNS
10_1101-436634	230	2	annotate	annotate	VBP
10_1101-436634	230	3	This	this	DT
10_1101-436634	230	4	command	command	NN
10_1101-436634	230	5	takes	take	VBZ
10_1101-436634	230	6	a	a	DT
10_1101-436634	230	7	list	list	NN
10_1101-436634	230	8	of	of	IN
10_1101-436634	230	9	variants	variant	NNS
10_1101-436634	230	10	in	in	IN
10_1101-436634	230	11	VCF	VCF	NNP
10_1101-436634	230	12	format	format	NN
10_1101-436634	230	13	.	.	.
10_1101-436634	231	1	The	the	DT
10_1101-436634	231	2	file	file	NN
10_1101-436634	231	3	should	should	MD
10_1101-436634	231	4	be	be	VB
10_1101-436634	231	5	gzipped	gzippe	VBN
10_1101-436634	231	6	and	and	CC
10_1101-436634	231	7	indexed	index	VBN
10_1101-436634	231	8	with	with	IN
10_1101-436634	231	9	Tabix46	Tabix46	NNP
10_1101-436634	231	10	.	.	.
10_1101-436634	232	1	The	the	DT
10_1101-436634	232	2	user	user	NN
10_1101-436634	232	3	must	must	MD
10_1101-436634	232	4	also	also	RB
10_1101-436634	232	5	supply	supply	VB
10_1101-436634	232	6	a	a	DT
10_1101-436634	232	7	GTF	gtf	NN
10_1101-436634	232	8	file	file	NN
10_1101-436634	232	9	that	that	WDT
10_1101-436634	232	10	specifies	specify	VBZ
10_1101-436634	232	11	the	the	DT
10_1101-436634	232	12	reference	reference	NN
10_1101-436634	232	13	transcriptome	transcriptome	DT
10_1101-436634	232	14	used	use	VBN
10_1101-436634	232	15	to	to	TO
10_1101-436634	232	16	annotate	annotate	VB
10_1101-436634	232	17	the	the	DT
10_1101-436634	232	18	variants	variant	NNS
10_1101-436634	232	19	.	.	.
10_1101-436634	233	1	The	the	DT
10_1101-436634	233	2	INFO	INFO	NNP
10_1101-436634	233	3	column	column	NN
10_1101-436634	233	4	of	of	IN
10_1101-436634	233	5	each	each	DT
10_1101-436634	233	6	line	line	NN
10_1101-436634	233	7	in	in	IN
10_1101-436634	233	8	the	the	DT
10_1101-436634	233	9	VCF	VCF	NNP
10_1101-436634	233	10	is	be	VBZ
10_1101-436634	233	11	populated	populate	VBN
10_1101-436634	233	12	with	with	IN
10_1101-436634	233	13	comma	comma	NN
10_1101-436634	233	14	-	-	HYPH
10_1101-436634	233	15	separated	separate	VBN
10_1101-436634	233	16	lists	list	NNS
10_1101-436634	233	17	of	of	IN
10_1101-436634	233	18	the	the	DT
10_1101-436634	233	19	variant	variant	JJ
10_1101-436634	233	20	-	-	HYPH
10_1101-436634	233	21	overlapping	overlap	VBG
10_1101-436634	233	22	genes	gene	NNS
10_1101-436634	233	23	,	,	,
10_1101-436634	233	24	variant	variant	JJ
10_1101-436634	233	25	-	-	HYPH
10_1101-436634	233	26	overlapping	overlapping	NN
10_1101-436634	233	27	transcripts	transcript	NNS
10_1101-436634	233	28	,	,	,
10_1101-436634	233	29	the	the	DT
10_1101-436634	233	30	distance	distance	NN
10_1101-436634	233	31	between	between	IN
10_1101-436634	233	32	the	the	DT
10_1101-436634	233	33	variant	variant	NN
10_1101-436634	233	34	and	and	CC
10_1101-436634	233	35	the	the	DT
10_1101-436634	233	36	associated	associate	VBN
10_1101-436634	233	37	exon	exon	NNP
10_1101-436634	233	38	edge	edge	NN
10_1101-436634	233	39	for	for	IN
10_1101-436634	233	40	each	each	DT
10_1101-436634	233	41	transcript	transcript	NN
10_1101-436634	233	42	(	(	-LRB-
10_1101-436634	233	43	i.e.	i.e.	FW
10_1101-436634	234	1	each	each	DT
10_1101-436634	234	2	start	start	NN
10_1101-436634	234	3	or	or	CC
10_1101-436634	234	4	end	end	NN
10_1101-436634	234	5	of	of	IN
10_1101-436634	234	6	an	an	DT
10_1101-436634	234	7	exon	exon	NN
10_1101-436634	234	8	whose	whose	WP$
10_1101-436634	234	9	splice	splice	NN
10_1101-436634	234	10	variant	variant	JJ
10_1101-436634	234	11	window	window	NN
10_1101-436634	234	12	included	include	VBD
10_1101-436634	234	13	the	the	DT
10_1101-436634	234	14	variant	variant	NN
10_1101-436634	234	15	)	)	-RRB-
10_1101-436634	234	16	defined	define	VBN
10_1101-436634	234	17	as	as	IN
10_1101-436634	234	18	min(distance_from_start_of_exon	min(distance_from_start_of_exon	NNP
10_1101-436634	234	19	,	,	,
10_1101-436634	234	20	distance_from_end_of_exon	distance_from_end_of_exon	NNP
10_1101-436634	234	21	)	)	-RRB-
10_1101-436634	234	22	,	,	,
10_1101-436634	234	23	and	and	CC
10_1101-436634	234	24	the	the	DT
10_1101-436634	234	25	variant	variant	JJ
10_1101-436634	234	26	type	type	NN
10_1101-436634	234	27	for	for	IN
10_1101-436634	234	28	each	each	DT
10_1101-436634	234	29	transcript	transcript	NN
10_1101-436634	234	30	.	.	.
10_1101-436634	235	1	Internally	internally	RB
10_1101-436634	235	2	,	,	,
10_1101-436634	235	3	this	this	DT
10_1101-436634	235	4	function	function	NN
10_1101-436634	235	5	relies	rely	VBZ
10_1101-436634	235	6	on	on	IN
10_1101-436634	235	7	HTSlib	HTSlib	NNP
10_1101-436634	235	8	to	to	TO
10_1101-436634	235	9	parse	parse	VB
10_1101-436634	235	10	the	the	DT
10_1101-436634	235	11	VCF	VCF	NNP
10_1101-436634	235	12	file	file	NN
10_1101-436634	235	13	and	and	CC
10_1101-436634	235	14	search	search	VB
10_1101-436634	235	15	for	for	IN
10_1101-436634	235	16	features	feature	NNS
10_1101-436634	235	17	in	in	IN
10_1101-436634	235	18	the	the	DT
10_1101-436634	235	19	GTF	GTF	NNP
10_1101-436634	235	20	file	file	NN
10_1101-436634	235	21	which	which	WDT
10_1101-436634	235	22	overlap	overlap	VBP
10_1101-436634	235	23	the	the	DT
10_1101-436634	235	24	variant	variant	NN
10_1101-436634	235	25	.	.	.
10_1101-436634	236	1	The	the	DT
10_1101-436634	236	2	splice	splice	NN
10_1101-436634	236	3	variant	variant	JJ
10_1101-436634	236	4	window	window	NN
10_1101-436634	236	5	size	size	NN
10_1101-436634	236	6	(	(	-LRB-
10_1101-436634	236	7	i.e.	i.e.	FW
10_1101-436634	237	1	the	the	DT
10_1101-436634	237	2	maximum	maximum	JJ
10_1101-436634	237	3	distance	distance	NN
10_1101-436634	237	4	from	from	IN
10_1101-436634	237	5	the	the	DT
10_1101-436634	237	6	edge	edge	NN
10_1101-436634	237	7	of	of	IN
10_1101-436634	237	8	an	an	DT
10_1101-436634	237	9	exon	exon	NN
10_1101-436634	237	10	used	use	VBN
10_1101-436634	237	11	to	to	TO
10_1101-436634	237	12	consider	consider	VB
10_1101-436634	237	13	a	a	DT
10_1101-436634	237	14	variant	variant	NN
10_1101-436634	237	15	as	as	IN
10_1101-436634	237	16	splicing	splicing	NN
10_1101-436634	237	17	-	-	HYPH
10_1101-436634	237	18	relevant	relevant	JJ
10_1101-436634	237	19	)	)	-RRB-
10_1101-436634	237	20	can	can	MD
10_1101-436634	237	21	be	be	VB
10_1101-436634	237	22	set	set	VBN
10_1101-436634	237	23	by	by	IN
10_1101-436634	237	24	the	the	DT
10_1101-436634	237	25	options	option	NNS
10_1101-436634	237	26	“	"	``
10_1101-436634	237	27	-	-	HYPH
10_1101-436634	237	28	e	e	NN
10_1101-436634	237	29	<	<	XX
10_1101-436634	237	30	number	number	NN
10_1101-436634	237	31	of	of	IN
10_1101-436634	237	32	bases	basis	NNS
10_1101-436634	237	33	>	>	XX
10_1101-436634	237	34	”	"	''
10_1101-436634	237	35	and	and	CC
10_1101-436634	237	36	“	"	``
10_1101-436634	237	37	-i	-i	:
10_1101-436634	237	38	<	<	XX
10_1101-436634	237	39	number	number	NN
10_1101-436634	237	40	of	of	IN
10_1101-436634	237	41	bases	basis	NNS
10_1101-436634	237	42	>	>	XX
10_1101-436634	237	43	”	"	''
10_1101-436634	237	44	for	for	IN
10_1101-436634	237	45	exonic	exonic	JJ
10_1101-436634	237	46	and	and	CC
10_1101-436634	237	47	intronic	intronic	JJ
10_1101-436634	237	48	variants	variant	NNS
10_1101-436634	237	49	,	,	,
10_1101-436634	237	50	respectively	respectively	RB
10_1101-436634	237	51	.	.	.
10_1101-436634	238	1	The	the	DT
10_1101-436634	238	2	variant	variant	JJ
10_1101-436634	238	3	type	type	NN
10_1101-436634	238	4	for	for	IN
10_1101-436634	238	5	each	each	DT
10_1101-436634	238	6	variant	variant	NN
10_1101-436634	238	7	thus	thus	RB
10_1101-436634	238	8	depends	depend	VBZ
10_1101-436634	238	9	on	on	IN
10_1101-436634	238	10	the	the	DT
10_1101-436634	238	11	options	option	NNS
10_1101-436634	238	12	used	use	VBN
10_1101-436634	238	13	to	to	TO
10_1101-436634	238	14	set	set	VB
10_1101-436634	238	15	the	the	DT
10_1101-436634	238	16	splice	splice	NN
10_1101-436634	238	17	variant	variant	JJ
10_1101-436634	238	18	window	window	NN
10_1101-436634	238	19	size	size	NN
10_1101-436634	238	20	.	.	.
10_1101-436634	239	1	Variants	variant	NNS
10_1101-436634	239	2	captured	capture	VBN
10_1101-436634	239	3	by	by	IN
10_1101-436634	239	4	the	the	DT
10_1101-436634	239	5	window	window	NN
10_1101-436634	239	6	set	set	VBN
10_1101-436634	239	7	by	by	IN
10_1101-436634	239	8	“	"	``
10_1101-436634	239	9	-e	-e	:
10_1101-436634	239	10	”	"	''
10_1101-436634	239	11	or	or	CC
10_1101-436634	239	12	“	"	``
10_1101-436634	239	13	-i	-i	:
10_1101-436634	239	14	”	"	''
10_1101-436634	239	15	are	be	VBP
10_1101-436634	239	16	annotated	annotate	VBN
10_1101-436634	239	17	as	as	IN
10_1101-436634	239	18	.CC	.CC	NFP
10_1101-436634	239	19	-	-	HYPH
10_1101-436634	239	20	BY	by	IN
10_1101-436634	239	21	-	-	HYPH
10_1101-436634	239	22	NC	NC	NNP
10_1101-436634	239	23	-	-	HYPH
10_1101-436634	239	24	ND	ND	NNP
10_1101-436634	239	25	4.0	4.0	CD
10_1101-436634	239	26	International	international	JJ
10_1101-436634	239	27	licensea	licensea	NNS
10_1101-436634	239	28	certified	certify	VBN
10_1101-436634	239	29	by	by	IN
10_1101-436634	239	30	peer	peer	NN
10_1101-436634	239	31	review	review	NN
10_1101-436634	239	32	)	)	-RRB-
10_1101-436634	239	33	is	be	VBZ
10_1101-436634	239	34	the	the	DT
10_1101-436634	239	35	author	author	NN
10_1101-436634	239	36	/	/	SYM
10_1101-436634	239	37	funder	funder	NN
10_1101-436634	239	38	,	,	,
10_1101-436634	239	39	who	who	WP
10_1101-436634	239	40	has	have	VBZ
10_1101-436634	239	41	granted	grant	VBN
10_1101-436634	239	42	bioRxiv	biorxiv	IN
10_1101-436634	239	43	a	a	DT
10_1101-436634	239	44	license	license	NN
10_1101-436634	239	45	to	to	TO
10_1101-436634	239	46	display	display	VB
10_1101-436634	239	47	the	the	DT
10_1101-436634	239	48	preprint	preprint	NN
10_1101-436634	239	49	in	in	IN
10_1101-436634	239	50	perpetuity	perpetuity	NN
10_1101-436634	239	51	.	.	.
10_1101-436634	240	1	It	-PRON-	PRP
10_1101-436634	240	2	is	be	VBZ
10_1101-436634	240	3	made	make	VBN
10_1101-436634	240	4	available	available	JJ
10_1101-436634	240	5	under	under	IN
10_1101-436634	240	6	The	the	DT
10_1101-436634	240	7	copyright	copyright	NN
10_1101-436634	240	8	holder	holder	NN
10_1101-436634	240	9	for	for	IN
10_1101-436634	240	10	this	this	DT
10_1101-436634	240	11	preprint	preprint	NN
10_1101-436634	240	12	(	(	-LRB-
10_1101-436634	240	13	which	which	WDT
10_1101-436634	240	14	was	be	VBD
10_1101-436634	240	15	notthis	notthis	DT
10_1101-436634	240	16	version	version	NN
10_1101-436634	240	17	posted	post	VBN
10_1101-436634	240	18	January	January	NNP
10_1101-436634	240	19	5	5	CD
10_1101-436634	240	20	,	,	,
10_1101-436634	240	21	2021	2021	CD
10_1101-436634	240	22	.	.	.
10_1101-436634	240	23	;	;	:
10_1101-436634	240	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	240	25	:	:	:
10_1101-436634	240	26	bioRxiv	biorxiv	VB
10_1101-436634	240	27	preprint	preprint	NN
10_1101-436634	240	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	240	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	240	30	12	12	CD
10_1101-436634	240	31	“	"	``
10_1101-436634	240	32	splicing_exonic	splicing_exonic	JJ
10_1101-436634	240	33	”	"	''
10_1101-436634	240	34	and	and	CC
10_1101-436634	240	35	“	"	``
10_1101-436634	240	36	splicing_intronic	splicing_intronic	JJ
10_1101-436634	240	37	”	"	''
10_1101-436634	240	38	,	,	,
10_1101-436634	240	39	respectively	respectively	RB
10_1101-436634	240	40	.	.	.
10_1101-436634	241	1	Alternatively	alternatively	RB
10_1101-436634	241	2	,	,	,
10_1101-436634	241	3	to	to	TO
10_1101-436634	241	4	analyze	analyze	VB
10_1101-436634	241	5	all	all	DT
10_1101-436634	241	6	exonic	exonic	JJ
10_1101-436634	241	7	or	or	CC
10_1101-436634	241	8	intronic	intronic	JJ
10_1101-436634	241	9	variants	variant	NNS
10_1101-436634	241	10	,	,	,
10_1101-436634	241	11	the	the	DT
10_1101-436634	241	12	“	"	``
10_1101-436634	241	13	-E	-E	:
10_1101-436634	241	14	”	"	''
10_1101-436634	241	15	and	and	CC
10_1101-436634	241	16	“	"	``
10_1101-436634	241	17	-I	-i	FW
10_1101-436634	241	18	”	"	''
10_1101-436634	241	19	options	option	NNS
10_1101-436634	241	20	can	can	MD
10_1101-436634	241	21	be	be	VB
10_1101-436634	241	22	used	use	VBN
10_1101-436634	241	23	.	.	.
10_1101-436634	242	1	Otherwise	otherwise	RB
10_1101-436634	242	2	,	,	,
10_1101-436634	242	3	the	the	DT
10_1101-436634	242	4	“	"	``
10_1101-436634	242	5	-E	-E	:
10_1101-436634	242	6	”	"	''
10_1101-436634	242	7	and	and	CC
10_1101-436634	242	8	“	"	``
10_1101-436634	242	9	-I	-i	FW
10_1101-436634	242	10	”	"	''
10_1101-436634	242	11	options	option	NNS
10_1101-436634	242	12	themselves	-PRON-	PRP
10_1101-436634	242	13	do	do	VBP
10_1101-436634	242	14	not	not	RB
10_1101-436634	242	15	change	change	VB
10_1101-436634	242	16	the	the	DT
10_1101-436634	242	17	variant	variant	JJ
10_1101-436634	242	18	type	type	NN
10_1101-436634	242	19	annotation	annotation	NN
10_1101-436634	242	20	,	,	,
10_1101-436634	242	21	and	and	CC
10_1101-436634	242	22	variants	variant	NNS
10_1101-436634	242	23	found	find	VBN
10_1101-436634	242	24	in	in	IN
10_1101-436634	242	25	these	these	DT
10_1101-436634	242	26	windows	window	NNS
10_1101-436634	242	27	are	be	VBP
10_1101-436634	242	28	labeled	label	VBN
10_1101-436634	242	29	simply	simply	RB
10_1101-436634	242	30	as	as	IN
10_1101-436634	242	31	“	"	``
10_1101-436634	242	32	exonic	exonic	JJ
10_1101-436634	242	33	”	"	''
10_1101-436634	242	34	or	or	CC
10_1101-436634	242	35	“	"	``
10_1101-436634	242	36	intronic	intronic	JJ
10_1101-436634	242	37	”	"	''
10_1101-436634	242	38	.	.	.
10_1101-436634	243	1	By	by	IN
10_1101-436634	243	2	default	default	NN
10_1101-436634	243	3	,	,	,
10_1101-436634	243	4	single	single	JJ
10_1101-436634	243	5	exon	exon	NN
10_1101-436634	243	6	transcripts	transcript	NNS
10_1101-436634	243	7	are	be	VBP
10_1101-436634	243	8	ignored	ignore	VBN
10_1101-436634	243	9	,	,	,
10_1101-436634	243	10	but	but	CC
10_1101-436634	243	11	they	-PRON-	PRP
10_1101-436634	243	12	can	can	MD
10_1101-436634	243	13	be	be	VB
10_1101-436634	243	14	included	include	VBN
10_1101-436634	243	15	with	with	IN
10_1101-436634	243	16	the	the	DT
10_1101-436634	243	17	“	"	``
10_1101-436634	243	18	-S	-S	NNP
10_1101-436634	243	19	”	"	''
10_1101-436634	243	20	option	option	NN
10_1101-436634	243	21	.	.	.
10_1101-436634	244	1	By	by	IN
10_1101-436634	244	2	default	default	NN
10_1101-436634	244	3	,	,	,
10_1101-436634	244	4	output	output	NN
10_1101-436634	244	5	is	be	VBZ
10_1101-436634	244	6	written	write	VBN
10_1101-436634	244	7	to	to	IN
10_1101-436634	244	8	STDOUT	STDOUT	NNP
10_1101-436634	244	9	in	in	IN
10_1101-436634	244	10	VCF	VCF	NNP
10_1101-436634	244	11	format	format	NN
10_1101-436634	244	12	.	.	.
10_1101-436634	245	1	To	to	TO
10_1101-436634	245	2	write	write	VB
10_1101-436634	245	3	to	to	IN
10_1101-436634	245	4	a	a	DT
10_1101-436634	245	5	file	file	NN
10_1101-436634	245	6	,	,	,
10_1101-436634	245	7	use	use	VB
10_1101-436634	245	8	the	the	DT
10_1101-436634	245	9	option	option	NN
10_1101-436634	245	10	“	"	``
10_1101-436634	245	11	-o	-o	NFP
10_1101-436634	245	12	<	<	XX
10_1101-436634	245	13	PATH	PATH	NNP
10_1101-436634	245	14	/	/	SYM
10_1101-436634	245	15	TO	TO	NNP
10_1101-436634	245	16	/	/	SYM
10_1101-436634	245	17	FILE	FILE	NNP
10_1101-436634	245	18	>	>	XX
10_1101-436634	245	19	”	"	''
10_1101-436634	245	20	.	.	.
10_1101-436634	246	1	Junctions	junction	NNS
10_1101-436634	246	2	extract	extract	VBP
10_1101-436634	246	3	This	this	DT
10_1101-436634	246	4	command	command	NN
10_1101-436634	246	5	takes	take	VBZ
10_1101-436634	246	6	an	an	DT
10_1101-436634	246	7	alignment	alignment	NN
10_1101-436634	246	8	file	file	NN
10_1101-436634	246	9	containing	contain	VBG
10_1101-436634	246	10	aligned	align	VBN
10_1101-436634	246	11	RNA	RNA	NNP
10_1101-436634	246	12	-	-	HYPH
10_1101-436634	246	13	seq	seq	NN
10_1101-436634	246	14	reads	read	NNS
10_1101-436634	246	15	and	and	CC
10_1101-436634	246	16	infers	infer	VBZ
10_1101-436634	246	17	junctions	junction	NNS
10_1101-436634	246	18	(	(	-LRB-
10_1101-436634	246	19	i.e.	i.e.	FW
10_1101-436634	247	1	exon	exon	NNP
10_1101-436634	247	2	-	-	HYPH
10_1101-436634	247	3	exon	exon	NN
10_1101-436634	247	4	boundaries	boundary	NNS
10_1101-436634	247	5	)	)	-RRB-
10_1101-436634	247	6	based	base	VBN
10_1101-436634	247	7	on	on	IN
10_1101-436634	247	8	skipped	skipped	JJ
10_1101-436634	247	9	regions	region	NNS
10_1101-436634	247	10	in	in	IN
10_1101-436634	247	11	alignments	alignment	NNS
10_1101-436634	247	12	as	as	IN
10_1101-436634	247	13	determined	determine	VBN
10_1101-436634	247	14	by	by	IN
10_1101-436634	247	15	the	the	DT
10_1101-436634	247	16	CIGAR	CIGAR	NNP
10_1101-436634	247	17	string	string	NN
10_1101-436634	247	18	operator	operator	NN
10_1101-436634	247	19	codes	code	NNS
10_1101-436634	247	20	.	.	.
10_1101-436634	248	1	These	these	DT
10_1101-436634	248	2	junctions	junction	NNS
10_1101-436634	248	3	are	be	VBP
10_1101-436634	248	4	written	write	VBN
10_1101-436634	248	5	to	to	IN
10_1101-436634	248	6	STDOUT	STDOUT	NNP
10_1101-436634	248	7	in	in	IN
10_1101-436634	248	8	BED12	BED12	NNP
10_1101-436634	248	9	format	format	NN
10_1101-436634	248	10	.	.	.
10_1101-436634	249	1	Alternatively	alternatively	RB
10_1101-436634	249	2	,	,	,
10_1101-436634	249	3	the	the	DT
10_1101-436634	249	4	output	output	NN
10_1101-436634	249	5	can	can	MD
10_1101-436634	249	6	be	be	VB
10_1101-436634	249	7	redirected	redirect	VBN
10_1101-436634	249	8	to	to	IN
10_1101-436634	249	9	a	a	DT
10_1101-436634	249	10	file	file	NN
10_1101-436634	249	11	with	with	IN
10_1101-436634	249	12	the	the	DT
10_1101-436634	249	13	“	"	``
10_1101-436634	249	14	-o	-o	NFP
10_1101-436634	249	15	<	<	XX
10_1101-436634	249	16	PATH	PATH	NNP
10_1101-436634	249	17	/	/	SYM
10_1101-436634	249	18	TO	TO	NNP
10_1101-436634	249	19	/	/	SYM
10_1101-436634	249	20	FILE	FILE	NNP
10_1101-436634	249	21	>	>	XX
10_1101-436634	249	22	”	"	''
10_1101-436634	249	23	.	.	.
10_1101-436634	250	1	RegTools	RegTools	NNP
10_1101-436634	250	2	ascertains	ascertain	NNS
10_1101-436634	250	3	strand	strand	NN
10_1101-436634	250	4	information	information	NN
10_1101-436634	250	5	based	base	VBN
10_1101-436634	250	6	on	on	IN
10_1101-436634	250	7	the	the	DT
10_1101-436634	250	8	XS	XS	NNP
10_1101-436634	250	9	tags	tag	NNS
10_1101-436634	250	10	set	set	VBN
10_1101-436634	250	11	by	by	IN
10_1101-436634	250	12	the	the	DT
10_1101-436634	250	13	aligner	aligner	NN
10_1101-436634	250	14	,	,	,
10_1101-436634	250	15	but	but	CC
10_1101-436634	250	16	can	can	MD
10_1101-436634	250	17	also	also	RB
10_1101-436634	250	18	determine	determine	VB
10_1101-436634	250	19	the	the	DT
10_1101-436634	250	20	inferred	inferred	JJ
10_1101-436634	250	21	strand	strand	NN
10_1101-436634	250	22	of	of	IN
10_1101-436634	250	23	transcription	transcription	NN
10_1101-436634	250	24	based	base	VBN
10_1101-436634	250	25	on	on	IN
10_1101-436634	250	26	the	the	DT
10_1101-436634	250	27	BAM	BAM	NNP
10_1101-436634	250	28	flags	flag	NNS
10_1101-436634	250	29	if	if	IN
10_1101-436634	250	30	a	a	DT
10_1101-436634	250	31	stranded	stranded	JJ
10_1101-436634	250	32	library	library	NN
10_1101-436634	250	33	strategy	strategy	NN
10_1101-436634	250	34	was	be	VBD
10_1101-436634	250	35	employed	employ	VBN
10_1101-436634	250	36	.	.	.
10_1101-436634	251	1	In	in	IN
10_1101-436634	251	2	the	the	DT
10_1101-436634	251	3	latter	latter	JJ
10_1101-436634	251	4	case	case	NN
10_1101-436634	251	5	,	,	,
10_1101-436634	251	6	the	the	DT
10_1101-436634	251	7	strand	strand	NNP
10_1101-436634	251	8	specificity	specificity	NN
10_1101-436634	251	9	of	of	IN
10_1101-436634	251	10	the	the	DT
10_1101-436634	251	11	library	library	NN
10_1101-436634	251	12	can	can	MD
10_1101-436634	251	13	be	be	VB
10_1101-436634	251	14	provided	provide	VBN
10_1101-436634	251	15	using	use	VBG
10_1101-436634	251	16	“	"	``
10_1101-436634	251	17	-s	-s	NFP
10_1101-436634	251	18	<	<	XX
10_1101-436634	251	19	INT	INT	NNP
10_1101-436634	251	20	>	>	XX
10_1101-436634	251	21	”	"	''
10_1101-436634	251	22	where	where	WRB
10_1101-436634	251	23	0	0	CD
10_1101-436634	251	24	=	=	SYM
10_1101-436634	251	25	unstranded	unstranded	JJ
10_1101-436634	251	26	,	,	,
10_1101-436634	251	27	1	1	CD
10_1101-436634	251	28	=	=	SYM
10_1101-436634	251	29	first	first	JJ
10_1101-436634	251	30	-	-	HYPH
10_1101-436634	251	31	strand	strand	NNP
10_1101-436634	251	32	/	/	SYM
10_1101-436634	251	33	RF	RF	NNP
10_1101-436634	251	34	,	,	,
10_1101-436634	251	35	2	2	CD
10_1101-436634	251	36	=	=	SYM
10_1101-436634	251	37	second	second	JJ
10_1101-436634	251	38	-	-	HYPH
10_1101-436634	251	39	strand	strand	NNP
10_1101-436634	251	40	/	/	SYM
10_1101-436634	251	41	FR	FR	NNP
10_1101-436634	251	42	.	.	.
10_1101-436634	252	1	We	-PRON-	PRP
10_1101-436634	252	2	suggest	suggest	VBP
10_1101-436634	252	3	that	that	IN
10_1101-436634	252	4	users	user	NNS
10_1101-436634	252	5	align	align	VBP
10_1101-436634	252	6	their	-PRON-	PRP$
10_1101-436634	252	7	RNA	RNA	NNP
10_1101-436634	252	8	-	-	HYPH
10_1101-436634	252	9	seq	seq	NN
10_1101-436634	252	10	data	datum	NNS
10_1101-436634	252	11	with	with	IN
10_1101-436634	252	12	HISAT230	HISAT230	NNP
10_1101-436634	252	13	,	,	,
10_1101-436634	252	14	TopHat231	TopHat231	NNP
10_1101-436634	252	15	,	,	,
10_1101-436634	252	16	or	or	CC
10_1101-436634	252	17	STAR29	STAR29	NNP
10_1101-436634	252	18	,	,	,
10_1101-436634	252	19	as	as	IN
10_1101-436634	252	20	these	these	DT
10_1101-436634	252	21	are	be	VBP
10_1101-436634	252	22	the	the	DT
10_1101-436634	252	23	aligners	aligner	NNS
10_1101-436634	252	24	we	-PRON-	PRP
10_1101-436634	252	25	have	have	VBP
10_1101-436634	252	26	tested	test	VBN
10_1101-436634	252	27	to	to	IN
10_1101-436634	252	28	date	date	NN
10_1101-436634	252	29	.	.	.
10_1101-436634	253	1	If	if	IN
10_1101-436634	253	2	RNA	RNA	NNP
10_1101-436634	253	3	-	-	HYPH
10_1101-436634	253	4	seq	seq	NN
10_1101-436634	253	5	data	datum	NNS
10_1101-436634	253	6	is	be	VBZ
10_1101-436634	253	7	unstranded	unstranded	JJ
10_1101-436634	253	8	and	and	CC
10_1101-436634	253	9	aligned	align	VBN
10_1101-436634	253	10	with	with	IN
10_1101-436634	253	11	STAR	STAR	NNP
10_1101-436634	253	12	,	,	,
10_1101-436634	253	13	users	user	NNS
10_1101-436634	253	14	must	must	MD
10_1101-436634	253	15	run	run	VB
10_1101-436634	253	16	STAR	STAR	NNP
10_1101-436634	253	17	with	with	IN
10_1101-436634	253	18	the	the	DT
10_1101-436634	253	19	--outSAMattributes	--outsamattributes	NN
10_1101-436634	253	20	option	option	NN
10_1101-436634	253	21	to	to	TO
10_1101-436634	253	22	include	include	VB
10_1101-436634	253	23	XS	XS	NNP
10_1101-436634	253	24	tags	tag	NNS
10_1101-436634	253	25	in	in	IN
10_1101-436634	253	26	the	the	DT
10_1101-436634	253	27	BAM	BAM	NNP
10_1101-436634	253	28	output	output	NN
10_1101-436634	253	29	.	.	.
10_1101-436634	254	1	Users	user	NNS
10_1101-436634	254	2	can	can	MD
10_1101-436634	254	3	set	set	VB
10_1101-436634	254	4	thresholds	threshold	NNS
10_1101-436634	254	5	for	for	IN
10_1101-436634	254	6	minimum	minimum	JJ
10_1101-436634	254	7	anchor	anchor	NN
10_1101-436634	254	8	length	length	NN
10_1101-436634	254	9	and	and	CC
10_1101-436634	254	10	minimum	minimum	NN
10_1101-436634	254	11	/	/	SYM
10_1101-436634	254	12	maximum	maximum	JJ
10_1101-436634	254	13	intron	intron	NNP
10_1101-436634	254	14	length	length	NN
10_1101-436634	254	15	.	.	.
10_1101-436634	255	1	The	the	DT
10_1101-436634	255	2	minimum	minimum	JJ
10_1101-436634	255	3	anchor	anchor	NN
10_1101-436634	255	4	length	length	NN
10_1101-436634	255	5	determines	determine	VBZ
10_1101-436634	255	6	how	how	WRB
10_1101-436634	255	7	many	many	JJ
10_1101-436634	255	8	contiguous	contiguous	JJ
10_1101-436634	255	9	,	,	,
10_1101-436634	255	10	matched	match	VBD
10_1101-436634	255	11	base	base	NN
10_1101-436634	255	12	pairs	pair	NNS
10_1101-436634	255	13	on	on	IN
10_1101-436634	255	14	either	either	DT
10_1101-436634	255	15	side	side	NN
10_1101-436634	255	16	of	of	IN
10_1101-436634	255	17	the	the	DT
10_1101-436634	255	18	junction	junction	NN
10_1101-436634	255	19	are	be	VBP
10_1101-436634	255	20	required	require	VBN
10_1101-436634	255	21	to	to	TO
10_1101-436634	255	22	include	include	VB
10_1101-436634	255	23	it	-PRON-	PRP
10_1101-436634	255	24	in	in	IN
10_1101-436634	255	25	the	the	DT
10_1101-436634	255	26	final	final	JJ
10_1101-436634	255	27	output	output	NN
10_1101-436634	255	28	.	.	.
10_1101-436634	256	1	The	the	DT
10_1101-436634	256	2	required	require	VBN
10_1101-436634	256	3	overlap	overlap	NN
10_1101-436634	256	4	can	can	MD
10_1101-436634	256	5	be	be	VB
10_1101-436634	256	6	observed	observe	VBN
10_1101-436634	256	7	amongst	amongst	IN
10_1101-436634	256	8	separated	separated	JJ
10_1101-436634	256	9	reads	read	NNS
10_1101-436634	256	10	,	,	,
10_1101-436634	256	11	whose	whose	WP$
10_1101-436634	256	12	union	union	NN
10_1101-436634	256	13	determines	determine	VBZ
10_1101-436634	256	14	the	the	DT
10_1101-436634	256	15	thickStart	thickstart	NN
10_1101-436634	256	16	and	and	CC
10_1101-436634	256	17	thickEnd	thickEnd	NNS
10_1101-436634	256	18	of	of	IN
10_1101-436634	256	19	the	the	DT
10_1101-436634	256	20	BED	BED	NNP
10_1101-436634	256	21	feature	feature	NN
10_1101-436634	256	22	.	.	.
10_1101-436634	257	1	By	by	IN
10_1101-436634	257	2	default	default	NN
10_1101-436634	257	3	,	,	,
10_1101-436634	257	4	a	a	DT
10_1101-436634	257	5	junction	junction	NN
10_1101-436634	257	6	must	must	MD
10_1101-436634	257	7	have	have	VB
10_1101-436634	257	8	8	8	CD
10_1101-436634	257	9	bp	bp	NN
10_1101-436634	257	10	anchors	anchor	NNS
10_1101-436634	257	11	on	on	IN
10_1101-436634	257	12	each	each	DT
10_1101-436634	257	13	side	side	NN
10_1101-436634	257	14	to	to	TO
10_1101-436634	257	15	be	be	VB
10_1101-436634	257	16	counted	count	VBN
10_1101-436634	257	17	but	but	CC
10_1101-436634	257	18	this	this	DT
10_1101-436634	257	19	can	can	MD
10_1101-436634	257	20	be	be	VB
10_1101-436634	257	21	set	set	VBN
10_1101-436634	257	22	using	use	VBG
10_1101-436634	257	23	the	the	DT
10_1101-436634	257	24	option	option	NN
10_1101-436634	257	25	“	"	``
10_1101-436634	257	26	-a	-a	:
10_1101-436634	257	27	<	<	XX
10_1101-436634	257	28	minimum	minimum	JJ
10_1101-436634	257	29	anchor	anchor	NN
10_1101-436634	257	30	length	length	NN
10_1101-436634	257	31	>	>	XX
10_1101-436634	257	32	”	"	''
10_1101-436634	257	33	.	.	.
10_1101-436634	258	1	The	the	DT
10_1101-436634	258	2	intron	intron	NN
10_1101-436634	258	3	length	length	NN
10_1101-436634	258	4	is	be	VBZ
10_1101-436634	258	5	simply	simply	RB
10_1101-436634	258	6	the	the	DT
10_1101-436634	258	7	end	end	NN
10_1101-436634	258	8	coordinate	coordinate	NN
10_1101-436634	258	9	of	of	IN
10_1101-436634	258	10	the	the	DT
10_1101-436634	258	11	junction	junction	NN
10_1101-436634	258	12	minus	minus	CC
10_1101-436634	258	13	the	the	DT
10_1101-436634	258	14	start	start	NN
10_1101-436634	258	15	coordinate	coordinate	JJ
10_1101-436634	258	16	.	.	.
10_1101-436634	259	1	By	by	IN
10_1101-436634	259	2	default	default	NN
10_1101-436634	259	3	,	,	,
10_1101-436634	259	4	the	the	DT
10_1101-436634	259	5	junction	junction	NN
10_1101-436634	259	6	must	must	MD
10_1101-436634	259	7	be	be	VB
10_1101-436634	259	8	between	between	IN
10_1101-436634	259	9	70	70	CD
10_1101-436634	259	10	bp	bp	NN
10_1101-436634	259	11	and	and	CC
10_1101-436634	259	12	500,000	500,000	CD
10_1101-436634	259	13	bp	bp	NN
10_1101-436634	259	14	,	,	,
10_1101-436634	259	15	but	but	CC
10_1101-436634	259	16	the	the	DT
10_1101-436634	259	17	minimum	minimum	NN
10_1101-436634	259	18	and	and	CC
10_1101-436634	259	19	maximum	maximum	NN
10_1101-436634	259	20	can	can	MD
10_1101-436634	259	21	be	be	VB
10_1101-436634	259	22	set	set	VBN
10_1101-436634	259	23	using	use	VBG
10_1101-436634	259	24	“	"	``
10_1101-436634	259	25	-i	-i	:
10_1101-436634	259	26	<	<	XX
10_1101-436634	259	27	minimum	minimum	JJ
10_1101-436634	259	28	intron	intron	NN
10_1101-436634	259	29	length	length	NN
10_1101-436634	259	30	>	>	XX
10_1101-436634	259	31	”	"	''
10_1101-436634	259	32	and	and	CC
10_1101-436634	259	33	“	"	``
10_1101-436634	259	34	-I	-i	ADD
10_1101-436634	259	35	<	<	XX
10_1101-436634	259	36	maximum	maximum	JJ
10_1101-436634	259	37	intron	intron	NNP
10_1101-436634	259	38	length	length	NNP
10_1101-436634	259	39	>	>	XX
10_1101-436634	259	40	”	"	''
10_1101-436634	259	41	,	,	,
10_1101-436634	259	42	respectively	respectively	RB
10_1101-436634	259	43	.	.	.
10_1101-436634	260	1	For	for	IN
10_1101-436634	260	2	efficiency	efficiency	NN
10_1101-436634	260	3	,	,	,
10_1101-436634	260	4	this	this	DT
10_1101-436634	260	5	tool	tool	NN
10_1101-436634	260	6	can	can	MD
10_1101-436634	260	7	be	be	VB
10_1101-436634	260	8	used	use	VBN
10_1101-436634	260	9	to	to	TO
10_1101-436634	260	10	process	process	VB
10_1101-436634	260	11	only	only	RB
10_1101-436634	260	12	alignments	alignment	VBZ
10_1101-436634	260	13	in	in	IN
10_1101-436634	260	14	a	a	DT
10_1101-436634	260	15	particular	particular	JJ
10_1101-436634	260	16	region	region	NN
10_1101-436634	260	17	as	as	IN
10_1101-436634	260	18	opposed	oppose	VBN
10_1101-436634	260	19	to	to	IN
10_1101-436634	260	20	analyzing	analyze	VBG
10_1101-436634	260	21	the	the	DT
10_1101-436634	260	22	entire	entire	JJ
10_1101-436634	260	23	BAM	bam	NN
10_1101-436634	260	24	file	file	NN
10_1101-436634	260	25	.	.	.
10_1101-436634	261	1	The	the	DT
10_1101-436634	261	2	option	option	NN
10_1101-436634	261	3	“	"	``
10_1101-436634	261	4	-r	-r	XX
10_1101-436634	261	5	<	<	XX
10_1101-436634	261	6	chr>:<start>-<stop	chr>:<start>-<stop	XX
10_1101-436634	261	7	>	>	XX
10_1101-436634	261	8	”	"	``
10_1101-436634	261	9	can	can	MD
10_1101-436634	261	10	be	be	VB
10_1101-436634	261	11	used	use	VBN
10_1101-436634	261	12	to	to	TO
10_1101-436634	261	13	set	set	VB
10_1101-436634	261	14	a	a	DT
10_1101-436634	261	15	single	single	JJ
10_1101-436634	261	16	contiguous	contiguous	JJ
10_1101-436634	261	17	region	region	NN
10_1101-436634	261	18	of	of	IN
10_1101-436634	261	19	interest	interest	NN
10_1101-436634	261	20	.	.	.
10_1101-436634	262	1	Multiple	multiple	JJ
10_1101-436634	262	2	jobs	job	NNS
10_1101-436634	262	3	can	can	MD
10_1101-436634	262	4	be	be	VB
10_1101-436634	262	5	run	run	VBN
10_1101-436634	262	6	in	in	IN
10_1101-436634	262	7	parallel	parallel	NN
10_1101-436634	262	8	to	to	TO
10_1101-436634	262	9	analyze	analyze	VB
10_1101-436634	262	10	separate	separate	JJ
10_1101-436634	262	11	non	non	JJ
10_1101-436634	262	12	-	-	JJ
10_1101-436634	262	13	contiguous	contiguous	JJ
10_1101-436634	262	14	regions	region	NNS
10_1101-436634	262	15	.	.	.
10_1101-436634	263	1	Junctions	junction	NNS
10_1101-436634	263	2	annotate	annotate	VBP
10_1101-436634	263	3	This	this	DT
10_1101-436634	263	4	command	command	NN
10_1101-436634	263	5	takes	take	VBZ
10_1101-436634	263	6	a	a	DT
10_1101-436634	263	7	list	list	NN
10_1101-436634	263	8	of	of	IN
10_1101-436634	263	9	junctions	junction	NNS
10_1101-436634	263	10	in	in	IN
10_1101-436634	263	11	BED12	BED12	NNP
10_1101-436634	263	12	format	format	NN
10_1101-436634	263	13	as	as	IN
10_1101-436634	263	14	input	input	NN
10_1101-436634	263	15	and	and	CC
10_1101-436634	263	16	annotates	annotate	VBZ
10_1101-436634	263	17	them	-PRON-	PRP
10_1101-436634	263	18	with	with	IN
10_1101-436634	263	19	respect	respect	NN
10_1101-436634	263	20	to	to	IN
10_1101-436634	263	21	a	a	DT
10_1101-436634	263	22	reference	reference	NN
10_1101-436634	263	23	transcriptome	transcriptome	VBN
10_1101-436634	263	24	in	in	IN
10_1101-436634	263	25	GTF	GTF	NNP
10_1101-436634	263	26	format	format	NN
10_1101-436634	263	27	.	.	.
10_1101-436634	264	1	The	the	DT
10_1101-436634	264	2	observed	observed	JJ
10_1101-436634	264	3	splice	splice	NN
10_1101-436634	264	4	-	-	HYPH
10_1101-436634	264	5	sites	site	NNS
10_1101-436634	264	6	used	use	VBN
10_1101-436634	264	7	are	be	VBP
10_1101-436634	264	8	recorded	record	VBN
10_1101-436634	264	9	based	base	VBN
10_1101-436634	264	10	on	on	IN
10_1101-436634	264	11	a	a	DT
10_1101-436634	264	12	reference	reference	NN
10_1101-436634	264	13	genome	genome	JJ
10_1101-436634	264	14	sequence	sequence	NN
10_1101-436634	264	15	in	in	IN
10_1101-436634	264	16	FASTA	FASTA	NNP
10_1101-436634	264	17	format	format	NN
10_1101-436634	264	18	.	.	.
10_1101-436634	265	1	The	the	DT
10_1101-436634	265	2	output	output	NN
10_1101-436634	265	3	is	be	VBZ
10_1101-436634	265	4	written	write	VBN
10_1101-436634	265	5	to	to	IN
10_1101-436634	265	6	STDOUT	STDOUT	NNP
10_1101-436634	265	7	in	in	IN
10_1101-436634	265	8	TSV	TSV	NNP
10_1101-436634	265	9	format	format	NN
10_1101-436634	265	10	,	,	,
10_1101-436634	265	11	with	with	IN
10_1101-436634	265	12	separate	separate	JJ
10_1101-436634	265	13	columns	column	NNS
10_1101-436634	265	14	for	for	IN
10_1101-436634	265	15	the	the	DT
10_1101-436634	265	16	number	number	NN
10_1101-436634	265	17	of	of	IN
10_1101-436634	265	18	splicing	splicing	NN
10_1101-436634	265	19	acceptors	acceptor	NNS
10_1101-436634	265	20	skipped	skip	VBD
10_1101-436634	265	21	,	,	,
10_1101-436634	265	22	number	number	NN
10_1101-436634	265	23	of	of	IN
10_1101-436634	265	24	splicing	splicing	NN
10_1101-436634	265	25	donors	donor	NNS
10_1101-436634	265	26	skipped	skip	VBD
10_1101-436634	265	27	,	,	,
10_1101-436634	265	28	number	number	NN
10_1101-436634	265	29	of	of	IN
10_1101-436634	265	30	exons	exon	NNS
10_1101-436634	265	31	skipped	skip	VBN
10_1101-436634	265	32	,	,	,
10_1101-436634	265	33	the	the	DT
10_1101-436634	265	34	junction	junction	NN
10_1101-436634	265	35	type	type	NN
10_1101-436634	265	36	,	,	,
10_1101-436634	265	37	whether	whether	IN
10_1101-436634	265	38	the	the	DT
10_1101-436634	265	39	donor	donor	NN
10_1101-436634	265	40	site	site	NN
10_1101-436634	265	41	is	be	VBZ
10_1101-436634	265	42	known	know	VBN
10_1101-436634	265	43	,	,	,
10_1101-436634	265	44	whether	whether	IN
10_1101-436634	265	45	the	the	DT
10_1101-436634	265	46	acceptor	acceptor	NN
10_1101-436634	265	47	site	site	NN
10_1101-436634	265	48	is	be	VBZ
10_1101-436634	265	49	known	know	VBN
10_1101-436634	265	50	,	,	,
10_1101-436634	265	51	whether	whether	IN
10_1101-436634	265	52	this	this	DT
10_1101-436634	265	53	junction	junction	NN
10_1101-436634	265	54	is	be	VBZ
10_1101-436634	265	55	known	know	VBN
10_1101-436634	265	56	,	,	,
10_1101-436634	265	57	the	the	DT
10_1101-436634	265	58	overlapping	overlapping	NN
10_1101-436634	265	59	transcripts	transcript	NNS
10_1101-436634	265	60	,	,	,
10_1101-436634	265	61	and	and	CC
10_1101-436634	265	62	the	the	DT
10_1101-436634	265	63	overlapping	overlap	VBG
10_1101-436634	265	64	genes	gene	NNS
10_1101-436634	265	65	,	,	,
10_1101-436634	265	66	in	in	IN
10_1101-436634	265	67	addition	addition	NN
10_1101-436634	265	68	to	to	IN
10_1101-436634	265	69	the	the	DT
10_1101-436634	265	70	chromosome	chromosome	NN
10_1101-436634	265	71	,	,	,
10_1101-436634	265	72	start	start	VB
10_1101-436634	265	73	,	,	,
10_1101-436634	265	74	stop	stop	VB
10_1101-436634	265	75	,	,	,
10_1101-436634	265	76	junction	junction	NN
10_1101-436634	265	77	name	name	NN
10_1101-436634	265	78	,	,	,
10_1101-436634	265	79	junction	junction	NN
10_1101-436634	265	80	score	score	NN
10_1101-436634	265	81	,	,	,
10_1101-436634	265	82	and	and	CC
10_1101-436634	265	83	strand	strand	NNP
10_1101-436634	265	84	taken	take	VBN
10_1101-436634	265	85	from	from	IN
10_1101-436634	265	86	the	the	DT
10_1101-436634	265	87	input	input	NN
10_1101-436634	265	88	BED12	BED12	NNP
10_1101-436634	265	89	file	file	NN
10_1101-436634	265	90	.	.	.
10_1101-436634	266	1	This	this	DT
10_1101-436634	266	2	output	output	NN
10_1101-436634	266	3	can	can	MD
10_1101-436634	266	4	be	be	VB
10_1101-436634	266	5	.CC	.CC	:
10_1101-436634	266	6	-	-	:
10_1101-436634	266	7	BY	by	IN
10_1101-436634	266	8	-	-	HYPH
10_1101-436634	266	9	NC	NC	NNP
10_1101-436634	266	10	-	-	HYPH
10_1101-436634	266	11	ND	ND	NNP
10_1101-436634	266	12	4.0	4.0	CD
10_1101-436634	266	13	International	international	JJ
10_1101-436634	266	14	licensea	licensea	NNS
10_1101-436634	266	15	certified	certify	VBN
10_1101-436634	266	16	by	by	IN
10_1101-436634	266	17	peer	peer	NN
10_1101-436634	266	18	review	review	NN
10_1101-436634	266	19	)	)	-RRB-
10_1101-436634	266	20	is	be	VBZ
10_1101-436634	266	21	the	the	DT
10_1101-436634	266	22	author	author	NN
10_1101-436634	266	23	/	/	SYM
10_1101-436634	266	24	funder	funder	NN
10_1101-436634	266	25	,	,	,
10_1101-436634	266	26	who	who	WP
10_1101-436634	266	27	has	have	VBZ
10_1101-436634	266	28	granted	grant	VBN
10_1101-436634	266	29	bioRxiv	biorxiv	IN
10_1101-436634	266	30	a	a	DT
10_1101-436634	266	31	license	license	NN
10_1101-436634	266	32	to	to	TO
10_1101-436634	266	33	display	display	VB
10_1101-436634	266	34	the	the	DT
10_1101-436634	266	35	preprint	preprint	NN
10_1101-436634	266	36	in	in	IN
10_1101-436634	266	37	perpetuity	perpetuity	NN
10_1101-436634	266	38	.	.	.
10_1101-436634	267	1	It	-PRON-	PRP
10_1101-436634	267	2	is	be	VBZ
10_1101-436634	267	3	made	make	VBN
10_1101-436634	267	4	available	available	JJ
10_1101-436634	267	5	under	under	IN
10_1101-436634	267	6	The	the	DT
10_1101-436634	267	7	copyright	copyright	NN
10_1101-436634	267	8	holder	holder	NN
10_1101-436634	267	9	for	for	IN
10_1101-436634	267	10	this	this	DT
10_1101-436634	267	11	preprint	preprint	NN
10_1101-436634	267	12	(	(	-LRB-
10_1101-436634	267	13	which	which	WDT
10_1101-436634	267	14	was	be	VBD
10_1101-436634	267	15	notthis	notthis	DT
10_1101-436634	267	16	version	version	NN
10_1101-436634	267	17	posted	post	VBN
10_1101-436634	267	18	January	January	NNP
10_1101-436634	267	19	5	5	CD
10_1101-436634	267	20	,	,	,
10_1101-436634	267	21	2021	2021	CD
10_1101-436634	267	22	.	.	.
10_1101-436634	267	23	;	;	:
10_1101-436634	267	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	267	25	:	:	:
10_1101-436634	267	26	bioRxiv	biorxiv	VB
10_1101-436634	267	27	preprint	preprint	NN
10_1101-436634	267	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	267	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	CD
10_1101-436634	267	30	13	13	CD
10_1101-436634	267	31	redirected	redirect	VBD
10_1101-436634	267	32	to	to	IN
10_1101-436634	267	33	a	a	DT
10_1101-436634	267	34	file	file	NN
10_1101-436634	267	35	with	with	IN
10_1101-436634	267	36	“	"	``
10_1101-436634	267	37	-o	-o	,
10_1101-436634	267	38	/PATH	/PATH	.
10_1101-436634	267	39	/	/	SYM
10_1101-436634	267	40	TO	TO	NNP
10_1101-436634	267	41	/	/	SYM
10_1101-436634	267	42	FILE	FILE	NNP
10_1101-436634	267	43	”	"	''
10_1101-436634	267	44	.	.	.
10_1101-436634	268	1	By	by	IN
10_1101-436634	268	2	default	default	NN
10_1101-436634	268	3	,	,	,
10_1101-436634	268	4	single	single	JJ
10_1101-436634	268	5	exon	exon	NN
10_1101-436634	268	6	transcripts	transcript	NNS
10_1101-436634	268	7	are	be	VBP
10_1101-436634	268	8	ignored	ignore	VBN
10_1101-436634	268	9	in	in	IN
10_1101-436634	268	10	the	the	DT
10_1101-436634	268	11	GTF	gtf	NN
10_1101-436634	268	12	but	but	CC
10_1101-436634	268	13	can	can	MD
10_1101-436634	268	14	be	be	VB
10_1101-436634	268	15	included	include	VBN
10_1101-436634	268	16	with	with	IN
10_1101-436634	268	17	the	the	DT
10_1101-436634	268	18	option	option	NN
10_1101-436634	268	19	“	"	``
10_1101-436634	268	20	-S	-S	NNP
10_1101-436634	268	21	”	"	''
10_1101-436634	268	22	.	.	.
10_1101-436634	269	1	Cis	Cis	NNP
10_1101-436634	269	2	-	-	HYPH
10_1101-436634	269	3	splice	splice	NN
10_1101-436634	269	4	-	-	HYPH
10_1101-436634	269	5	effects	effect	NNS
10_1101-436634	269	6	identify	identify	VBP
10_1101-436634	269	7	This	this	DT
10_1101-436634	269	8	command	command	NN
10_1101-436634	269	9	combines	combine	VBZ
10_1101-436634	269	10	the	the	DT
10_1101-436634	269	11	above	above	JJ
10_1101-436634	269	12	utilities	utility	NNS
10_1101-436634	269	13	into	into	IN
10_1101-436634	269	14	a	a	DT
10_1101-436634	269	15	pipeline	pipeline	NN
10_1101-436634	269	16	for	for	IN
10_1101-436634	269	17	identifying	identify	VBG
10_1101-436634	269	18	variants	variant	NNS
10_1101-436634	269	19	which	which	WDT
10_1101-436634	269	20	may	may	MD
10_1101-436634	269	21	cause	cause	VB
10_1101-436634	269	22	aberrant	aberrant	JJ
10_1101-436634	269	23	splicing	splicing	NN
10_1101-436634	269	24	events	event	NNS
10_1101-436634	269	25	by	by	IN
10_1101-436634	269	26	altering	alter	VBG
10_1101-436634	269	27	splicing	splicing	NN
10_1101-436634	269	28	motifs	motif	NNS
10_1101-436634	269	29	in	in	IN
10_1101-436634	269	30	cis	cis	NNP
10_1101-436634	269	31	.	.	.
10_1101-436634	270	1	As	as	IN
10_1101-436634	270	2	such	such	JJ
10_1101-436634	270	3	,	,	,
10_1101-436634	270	4	it	-PRON-	PRP
10_1101-436634	270	5	relies	rely	VBZ
10_1101-436634	270	6	on	on	IN
10_1101-436634	270	7	essentially	essentially	RB
10_1101-436634	270	8	the	the	DT
10_1101-436634	270	9	same	same	JJ
10_1101-436634	270	10	inputs	input	NNS
10_1101-436634	270	11	:	:	:
10_1101-436634	270	12	a	a	DT
10_1101-436634	270	13	gzipped	gzipped	JJ
10_1101-436634	270	14	and	and	CC
10_1101-436634	270	15	Tabix	Tabix	NNP
10_1101-436634	270	16	-	-	HYPH
10_1101-436634	270	17	indexed	index	VBN
10_1101-436634	270	18	VCF	VCF	NNP
10_1101-436634	270	19	file	file	NN
10_1101-436634	270	20	containing	contain	VBG
10_1101-436634	270	21	a	a	DT
10_1101-436634	270	22	list	list	NN
10_1101-436634	270	23	of	of	IN
10_1101-436634	270	24	variants	variant	NNS
10_1101-436634	270	25	,	,	,
10_1101-436634	270	26	an	an	DT
10_1101-436634	270	27	alignment	alignment	NN
10_1101-436634	270	28	file	file	NN
10_1101-436634	270	29	containing	contain	VBG
10_1101-436634	270	30	aligned	align	VBN
10_1101-436634	270	31	RNA	RNA	NNP
10_1101-436634	270	32	-	-	HYPH
10_1101-436634	270	33	seq	seq	NN
10_1101-436634	270	34	reads	read	NNS
10_1101-436634	270	35	,	,	,
10_1101-436634	270	36	a	a	DT
10_1101-436634	270	37	GTF	gtf	NN
10_1101-436634	270	38	file	file	NN
10_1101-436634	270	39	containing	contain	VBG
10_1101-436634	270	40	the	the	DT
10_1101-436634	270	41	reference	reference	NN
10_1101-436634	270	42	transcriptome	transcriptome	DT
10_1101-436634	270	43	of	of	IN
10_1101-436634	270	44	interest	interest	NN
10_1101-436634	270	45	,	,	,
10_1101-436634	270	46	and	and	CC
10_1101-436634	270	47	a	a	DT
10_1101-436634	270	48	FASTA	FASTA	NNP
10_1101-436634	270	49	file	file	NN
10_1101-436634	270	50	containing	contain	VBG
10_1101-436634	270	51	the	the	DT
10_1101-436634	270	52	reference	reference	NN
10_1101-436634	270	53	genome	genome	JJ
10_1101-436634	270	54	sequence	sequence	NN
10_1101-436634	270	55	of	of	IN
10_1101-436634	270	56	interest	interest	NN
10_1101-436634	270	57	.	.	.
10_1101-436634	271	1	First	first	RB
10_1101-436634	271	2	,	,	,
10_1101-436634	271	3	the	the	DT
10_1101-436634	271	4	list	list	NN
10_1101-436634	271	5	of	of	IN
10_1101-436634	271	6	variants	variant	NNS
10_1101-436634	271	7	is	be	VBZ
10_1101-436634	271	8	annotated	annotate	VBN
10_1101-436634	271	9	.	.	.
10_1101-436634	272	1	The	the	DT
10_1101-436634	272	2	splice	splice	NN
10_1101-436634	272	3	variant	variant	JJ
10_1101-436634	272	4	window	window	NN
10_1101-436634	272	5	size	size	NN
10_1101-436634	272	6	is	be	VBZ
10_1101-436634	272	7	set	set	VBN
10_1101-436634	272	8	using	use	VBG
10_1101-436634	272	9	the	the	DT
10_1101-436634	272	10	options	option	NNS
10_1101-436634	272	11	“	"	``
10_1101-436634	272	12	-	-	HYPH
10_1101-436634	272	13	e	e	NN
10_1101-436634	272	14	”	"	''
10_1101-436634	272	15	,	,	,
10_1101-436634	272	16	“	"	``
10_1101-436634	272	17	-i	-i	:
10_1101-436634	272	18	”	"	''
10_1101-436634	272	19	,	,	,
10_1101-436634	272	20	“	"	``
10_1101-436634	272	21	-E	-E	:
10_1101-436634	272	22	”	"	''
10_1101-436634	272	23	,	,	,
10_1101-436634	272	24	and	and	CC
10_1101-436634	272	25	“	"	``
10_1101-436634	272	26	-I	-i	FW
10_1101-436634	272	27	”	"	''
10_1101-436634	272	28	,	,	,
10_1101-436634	272	29	just	just	RB
10_1101-436634	272	30	as	as	IN
10_1101-436634	272	31	in	in	IN
10_1101-436634	272	32	variants	variant	NNS
10_1101-436634	272	33	annotate	annotate	JJ
10_1101-436634	272	34	.	.	.
10_1101-436634	273	1	The	the	DT
10_1101-436634	273	2	splice	splice	NN
10_1101-436634	273	3	junction	junction	NN
10_1101-436634	273	4	region	region	NN
10_1101-436634	273	5	size	size	NN
10_1101-436634	273	6	(	(	-LRB-
10_1101-436634	273	7	i.e.	i.e.	FW
10_1101-436634	274	1	the	the	DT
10_1101-436634	274	2	range	range	NN
10_1101-436634	274	3	around	around	IN
10_1101-436634	274	4	a	a	DT
10_1101-436634	274	5	particular	particular	JJ
10_1101-436634	274	6	variant	variant	NN
10_1101-436634	274	7	in	in	IN
10_1101-436634	274	8	which	which	WDT
10_1101-436634	274	9	an	an	DT
10_1101-436634	274	10	overlapping	overlap	VBG
10_1101-436634	274	11	junction	junction	NN
10_1101-436634	274	12	is	be	VBZ
10_1101-436634	274	13	associated	associate	VBN
10_1101-436634	274	14	with	with	IN
10_1101-436634	274	15	the	the	DT
10_1101-436634	274	16	variant	variant	NN
10_1101-436634	274	17	)	)	-RRB-
10_1101-436634	274	18	can	can	MD
10_1101-436634	274	19	be	be	VB
10_1101-436634	274	20	set	set	VBN
10_1101-436634	274	21	using	use	VBG
10_1101-436634	274	22	“	"	``
10_1101-436634	274	23	-w	-w	:
10_1101-436634	274	24	<	<	XX
10_1101-436634	274	25	splice	splice	NN
10_1101-436634	274	26	junction	junction	NN
10_1101-436634	274	27	region	region	NN
10_1101-436634	274	28	size	size	NN
10_1101-436634	274	29	>	>	XX
10_1101-436634	274	30	”	"	''
10_1101-436634	274	31	.	.	.
10_1101-436634	275	1	By	by	IN
10_1101-436634	275	2	default	default	NN
10_1101-436634	275	3	,	,	,
10_1101-436634	275	4	this	this	DT
10_1101-436634	275	5	range	range	NN
10_1101-436634	275	6	is	be	VBZ
10_1101-436634	275	7	not	not	RB
10_1101-436634	275	8	a	a	DT
10_1101-436634	275	9	particular	particular	JJ
10_1101-436634	275	10	number	number	NN
10_1101-436634	275	11	of	of	IN
10_1101-436634	275	12	bases	basis	NNS
10_1101-436634	275	13	but	but	CC
10_1101-436634	275	14	is	be	VBZ
10_1101-436634	275	15	calculated	calculate	VBN
10_1101-436634	275	16	individually	individually	RB
10_1101-436634	275	17	for	for	IN
10_1101-436634	275	18	each	each	DT
10_1101-436634	275	19	variant	variant	JJ
10_1101-436634	275	20	,	,	,
10_1101-436634	275	21	depending	depend	VBG
10_1101-436634	275	22	on	on	IN
10_1101-436634	275	23	the	the	DT
10_1101-436634	275	24	variant	variant	JJ
10_1101-436634	275	25	type	type	NN
10_1101-436634	275	26	annotation	annotation	NN
10_1101-436634	275	27	.	.	.
10_1101-436634	276	1	For	for	IN
10_1101-436634	276	2	“	"	``
10_1101-436634	276	3	splicing_exonic	splicing_exonic	JJ
10_1101-436634	276	4	”	"	''
10_1101-436634	276	5	,	,	,
10_1101-436634	276	6	“	"	``
10_1101-436634	276	7	splicing_intronic	splicing_intronic	JJ
10_1101-436634	276	8	”	"	''
10_1101-436634	276	9	,	,	,
10_1101-436634	276	10	and	and	CC
10_1101-436634	276	11	“	"	``
10_1101-436634	276	12	exonic	exonic	JJ
10_1101-436634	276	13	”	"	''
10_1101-436634	276	14	variants	variant	NNS
10_1101-436634	276	15	,	,	,
10_1101-436634	276	16	the	the	DT
10_1101-436634	276	17	region	region	NN
10_1101-436634	276	18	extends	extend	VBZ
10_1101-436634	276	19	from	from	IN
10_1101-436634	276	20	the	the	DT
10_1101-436634	276	21	3	3	CD
10_1101-436634	276	22	’	'	''
10_1101-436634	276	23	end	end	NN
10_1101-436634	276	24	of	of	IN
10_1101-436634	276	25	the	the	DT
10_1101-436634	276	26	exon	exon	NN
10_1101-436634	276	27	directly	directly	RB
10_1101-436634	276	28	upstream	upstream	JJ
10_1101-436634	276	29	of	of	IN
10_1101-436634	276	30	the	the	DT
10_1101-436634	276	31	variant	variant	NN
10_1101-436634	276	32	-	-	HYPH
10_1101-436634	276	33	associated	associate	VBN
10_1101-436634	276	34	exon	exon	NNP
10_1101-436634	276	35	to	to	IN
10_1101-436634	276	36	the	the	DT
10_1101-436634	276	37	5	5	CD
10_1101-436634	276	38	’	'	''
10_1101-436634	276	39	end	end	NN
10_1101-436634	276	40	of	of	IN
10_1101-436634	276	41	the	the	DT
10_1101-436634	276	42	exon	exon	NN
10_1101-436634	276	43	directly	directly	RB
10_1101-436634	276	44	downstream	downstream	JJ
10_1101-436634	276	45	of	of	IN
10_1101-436634	276	46	it	-PRON-	PRP
10_1101-436634	276	47	.	.	.
10_1101-436634	277	1	For	for	IN
10_1101-436634	277	2	“	"	``
10_1101-436634	277	3	intronic	intronic	JJ
10_1101-436634	277	4	”	"	''
10_1101-436634	277	5	variants	variant	NNS
10_1101-436634	277	6	,	,	,
10_1101-436634	277	7	the	the	DT
10_1101-436634	277	8	region	region	NN
10_1101-436634	277	9	is	be	VBZ
10_1101-436634	277	10	limited	limit	VBN
10_1101-436634	277	11	to	to	IN
10_1101-436634	277	12	the	the	DT
10_1101-436634	277	13	intron	intron	NN
10_1101-436634	277	14	containing	contain	VBG
10_1101-436634	277	15	the	the	DT
10_1101-436634	277	16	variant	variant	NN
10_1101-436634	277	17	.	.	.
10_1101-436634	278	1	Single	single	JJ
10_1101-436634	278	2	-	-	HYPH
10_1101-436634	278	3	exons	exon	NNS
10_1101-436634	278	4	can	can	MD
10_1101-436634	278	5	be	be	VB
10_1101-436634	278	6	kept	keep	VBN
10_1101-436634	278	7	with	with	IN
10_1101-436634	278	8	the	the	DT
10_1101-436634	278	9	“	"	``
10_1101-436634	278	10	-S	-S	NNP
10_1101-436634	278	11	”	"	''
10_1101-436634	278	12	option	option	NN
10_1101-436634	278	13	.	.	.
10_1101-436634	279	1	The	the	DT
10_1101-436634	279	2	annotated	annotate	VBN
10_1101-436634	279	3	list	list	NN
10_1101-436634	279	4	of	of	IN
10_1101-436634	279	5	variants	variant	NNS
10_1101-436634	279	6	in	in	IN
10_1101-436634	279	7	VCF	VCF	NNP
10_1101-436634	279	8	format	format	NN
10_1101-436634	279	9	(	(	-LRB-
10_1101-436634	279	10	analogous	analogous	JJ
10_1101-436634	279	11	to	to	IN
10_1101-436634	279	12	the	the	DT
10_1101-436634	279	13	output	output	NN
10_1101-436634	279	14	of	of	IN
10_1101-436634	279	15	variants	variant	NNS
10_1101-436634	279	16	annotate	annotate	JJ
10_1101-436634	279	17	)	)	-RRB-
10_1101-436634	279	18	can	can	MD
10_1101-436634	279	19	be	be	VB
10_1101-436634	279	20	written	write	VBN
10_1101-436634	279	21	to	to	IN
10_1101-436634	279	22	a	a	DT
10_1101-436634	279	23	file	file	NN
10_1101-436634	279	24	with	with	IN
10_1101-436634	279	25	“	"	``
10_1101-436634	279	26	-v	-v	-RRB-
10_1101-436634	279	27	/PATH	/PATH	.
10_1101-436634	279	28	/	/	SYM
10_1101-436634	279	29	TO	TO	NNP
10_1101-436634	279	30	/	/	SYM
10_1101-436634	279	31	FILE	FILE	NNP
10_1101-436634	279	32	”	"	''
10_1101-436634	279	33	.	.	.
10_1101-436634	280	1	The	the	DT
10_1101-436634	280	2	BAM	bam	NN
10_1101-436634	280	3	file	file	NN
10_1101-436634	280	4	is	be	VBZ
10_1101-436634	280	5	then	then	RB
10_1101-436634	280	6	processed	process	VBN
10_1101-436634	280	7	in	in	IN
10_1101-436634	280	8	the	the	DT
10_1101-436634	280	9	splice	splice	NN
10_1101-436634	280	10	junction	junction	NN
10_1101-436634	280	11	regions	region	NNS
10_1101-436634	280	12	to	to	TO
10_1101-436634	280	13	produce	produce	VB
10_1101-436634	280	14	the	the	DT
10_1101-436634	280	15	list	list	NN
10_1101-436634	280	16	of	of	IN
10_1101-436634	280	17	junctions	junction	NNS
10_1101-436634	280	18	.	.	.
10_1101-436634	281	1	A	a	DT
10_1101-436634	281	2	file	file	NN
10_1101-436634	281	3	containing	contain	VBG
10_1101-436634	281	4	these	these	DT
10_1101-436634	281	5	junctions	junction	NNS
10_1101-436634	281	6	in	in	IN
10_1101-436634	281	7	BED12	BED12	NNP
10_1101-436634	281	8	format	format	NN
10_1101-436634	281	9	(	(	-LRB-
10_1101-436634	281	10	analogous	analogous	JJ
10_1101-436634	281	11	to	to	IN
10_1101-436634	281	12	the	the	DT
10_1101-436634	281	13	output	output	NN
10_1101-436634	281	14	of	of	IN
10_1101-436634	281	15	junctions	junction	NNS
10_1101-436634	281	16	extract	extract	NN
10_1101-436634	281	17	)	)	-RRB-
10_1101-436634	281	18	can	can	MD
10_1101-436634	281	19	be	be	VB
10_1101-436634	281	20	written	write	VBN
10_1101-436634	281	21	using	use	VBG
10_1101-436634	281	22	“	"	``
10_1101-436634	281	23	-j	-j	:
10_1101-436634	281	24	/PATH	/PATH	.
10_1101-436634	281	25	/	/	SYM
10_1101-436634	281	26	TO	TO	NNP
10_1101-436634	281	27	/	/	SYM
10_1101-436634	281	28	FILE	FILE	NNP
10_1101-436634	281	29	”	"	''
10_1101-436634	281	30	.	.	.
10_1101-436634	282	1	The	the	DT
10_1101-436634	282	2	minimum	minimum	JJ
10_1101-436634	282	3	anchor	anchor	NN
10_1101-436634	282	4	length	length	NN
10_1101-436634	282	5	,	,	,
10_1101-436634	282	6	minimum	minimum	JJ
10_1101-436634	282	7	intron	intron	NN
10_1101-436634	282	8	length	length	NN
10_1101-436634	282	9	,	,	,
10_1101-436634	282	10	and	and	CC
10_1101-436634	282	11	maximum	maximum	JJ
10_1101-436634	282	12	intron	intron	NNP
10_1101-436634	282	13	length	length	NN
10_1101-436634	282	14	can	can	MD
10_1101-436634	282	15	be	be	VB
10_1101-436634	282	16	set	set	VBN
10_1101-436634	282	17	using	use	VBG
10_1101-436634	282	18	“	"	``
10_1101-436634	282	19	-a	-a	NN
10_1101-436634	282	20	”	"	''
10_1101-436634	282	21	,	,	,
10_1101-436634	282	22	“	"	``
10_1101-436634	282	23	-i	-i	:
10_1101-436634	282	24	”	"	''
10_1101-436634	282	25	,	,	,
10_1101-436634	282	26	and	and	CC
10_1101-436634	282	27	“	"	``
10_1101-436634	282	28	-I	-i	FW
10_1101-436634	282	29	”	"	''
10_1101-436634	282	30	options	option	NNS
10_1101-436634	282	31	,	,	,
10_1101-436634	282	32	just	just	RB
10_1101-436634	282	33	as	as	IN
10_1101-436634	282	34	in	in	IN
10_1101-436634	282	35	junctions	junction	NNS
10_1101-436634	282	36	extract	extract	NNP
10_1101-436634	282	37	.	.	.
10_1101-436634	283	1	The	the	DT
10_1101-436634	283	2	list	list	NN
10_1101-436634	283	3	of	of	IN
10_1101-436634	283	4	junctions	junction	NNS
10_1101-436634	283	5	produced	produce	VBN
10_1101-436634	283	6	by	by	IN
10_1101-436634	283	7	the	the	DT
10_1101-436634	283	8	preceding	precede	VBG
10_1101-436634	283	9	step	step	NN
10_1101-436634	283	10	is	be	VBZ
10_1101-436634	283	11	then	then	RB
10_1101-436634	283	12	annotated	annotate	VBN
10_1101-436634	283	13	with	with	IN
10_1101-436634	283	14	the	the	DT
10_1101-436634	283	15	information	information	NN
10_1101-436634	283	16	presented	present	VBN
10_1101-436634	283	17	in	in	IN
10_1101-436634	283	18	junctions	junction	NNS
10_1101-436634	283	19	annotate	annotate	JJ
10_1101-436634	283	20	.	.	.
10_1101-436634	284	1	Additionally	additionally	RB
10_1101-436634	284	2	,	,	,
10_1101-436634	284	3	each	each	DT
10_1101-436634	284	4	junction	junction	NN
10_1101-436634	284	5	is	be	VBZ
10_1101-436634	284	6	annotated	annotate	VBN
10_1101-436634	284	7	with	with	IN
10_1101-436634	284	8	a	a	DT
10_1101-436634	284	9	list	list	NN
10_1101-436634	284	10	of	of	IN
10_1101-436634	284	11	associated	associated	JJ
10_1101-436634	284	12	variants	variant	NNS
10_1101-436634	284	13	(	(	-LRB-
10_1101-436634	284	14	i.e.	i.e.	FW
10_1101-436634	285	1	variants	variant	NNS
10_1101-436634	285	2	whose	whose	WP$
10_1101-436634	285	3	splice	splice	NN
10_1101-436634	285	4	junction	junction	NN
10_1101-436634	285	5	regions	region	NNS
10_1101-436634	285	6	overlapped	overlap	VBD
10_1101-436634	285	7	the	the	DT
10_1101-436634	285	8	junction	junction	NN
10_1101-436634	285	9	)	)	-RRB-
10_1101-436634	285	10	.	.	.
10_1101-436634	286	1	The	the	DT
10_1101-436634	286	2	final	final	JJ
10_1101-436634	286	3	output	output	NN
10_1101-436634	286	4	is	be	VBZ
10_1101-436634	286	5	written	write	VBN
10_1101-436634	286	6	to	to	IN
10_1101-436634	286	7	STDOUT	STDOUT	NNP
10_1101-436634	286	8	in	in	IN
10_1101-436634	286	9	TSV	TSV	NNP
10_1101-436634	286	10	format	format	NN
10_1101-436634	286	11	(	(	-LRB-
10_1101-436634	286	12	analogous	analogous	JJ
10_1101-436634	286	13	to	to	IN
10_1101-436634	286	14	the	the	DT
10_1101-436634	286	15	output	output	NN
10_1101-436634	286	16	of	of	IN
10_1101-436634	286	17	junctions	junction	NNS
10_1101-436634	286	18	annotate	annotate	JJ
10_1101-436634	286	19	)	)	-RRB-
10_1101-436634	286	20	or	or	CC
10_1101-436634	286	21	can	can	MD
10_1101-436634	286	22	be	be	VB
10_1101-436634	286	23	redirected	redirect	VBN
10_1101-436634	286	24	to	to	IN
10_1101-436634	286	25	a	a	DT
10_1101-436634	286	26	file	file	NN
10_1101-436634	286	27	with	with	IN
10_1101-436634	286	28	“	"	``
10_1101-436634	286	29	-o	-o	,
10_1101-436634	286	30	/PATH	/PATH	.
10_1101-436634	286	31	/	/	SYM
10_1101-436634	286	32	TO	TO	NNP
10_1101-436634	286	33	/	/	SYM
10_1101-436634	286	34	FILE	FILE	NNP
10_1101-436634	286	35	”	"	''
10_1101-436634	286	36	.	.	.
10_1101-436634	287	1	Cis	Cis	NNP
10_1101-436634	287	2	-	-	HYPH
10_1101-436634	287	3	splice	splice	NN
10_1101-436634	287	4	-	-	HYPH
10_1101-436634	287	5	effects	effect	NNS
10_1101-436634	287	6	associate	associate	NN
10_1101-436634	287	7	This	this	DT
10_1101-436634	287	8	command	command	NN
10_1101-436634	287	9	is	be	VBZ
10_1101-436634	287	10	similar	similar	JJ
10_1101-436634	287	11	to	to	IN
10_1101-436634	287	12	cis	cis	NN
10_1101-436634	287	13	-	-	HYPH
10_1101-436634	287	14	splice	splice	NN
10_1101-436634	287	15	-	-	HYPH
10_1101-436634	287	16	effects	effect	NNS
10_1101-436634	287	17	identify	identify	VBP
10_1101-436634	287	18	,	,	,
10_1101-436634	287	19	but	but	CC
10_1101-436634	287	20	takes	take	VBZ
10_1101-436634	287	21	the	the	DT
10_1101-436634	287	22	BED	BED	NNP
10_1101-436634	287	23	output	output	NN
10_1101-436634	287	24	of	of	IN
10_1101-436634	287	25	junctions	junction	NNS
10_1101-436634	287	26	extract	extract	VBP
10_1101-436634	287	27	in	in	IN
10_1101-436634	287	28	lieu	lieu	NN
10_1101-436634	287	29	of	of	IN
10_1101-436634	287	30	an	an	DT
10_1101-436634	287	31	alignment	alignment	NN
10_1101-436634	287	32	file	file	NN
10_1101-436634	287	33	with	with	IN
10_1101-436634	287	34	RNA	RNA	NNP
10_1101-436634	287	35	alignments	alignment	NNS
10_1101-436634	287	36	.	.	.
10_1101-436634	288	1	As	as	IN
10_1101-436634	288	2	with	with	IN
10_1101-436634	288	3	cis	cis	NN
10_1101-436634	288	4	-	-	HYPH
10_1101-436634	288	5	splice	splice	NN
10_1101-436634	288	6	-	-	HYPH
10_1101-436634	288	7	effects	effect	NNS
10_1101-436634	288	8	identify	identify	VBP
10_1101-436634	288	9	,	,	,
10_1101-436634	288	10	each	each	DT
10_1101-436634	288	11	junction	junction	NN
10_1101-436634	288	12	is	be	VBZ
10_1101-436634	288	13	annotated	annotate	VBN
10_1101-436634	288	14	with	with	IN
10_1101-436634	288	15	a	a	DT
10_1101-436634	288	16	list	list	NN
10_1101-436634	288	17	of	of	IN
10_1101-436634	288	18	associated	associated	JJ
10_1101-436634	288	19	variants	variant	NNS
10_1101-436634	288	20	(	(	-LRB-
10_1101-436634	288	21	i.e.	i.e.	FW
10_1101-436634	289	1	variants	variant	NNS
10_1101-436634	289	2	whose	whose	WP$
10_1101-436634	289	3	splice	splice	NN
10_1101-436634	289	4	junction	junction	NN
10_1101-436634	289	5	regions	region	NNS
10_1101-436634	289	6	overlapped	overlap	VBD
10_1101-436634	289	7	the	the	DT
10_1101-436634	289	8	junction	junction	NN
10_1101-436634	289	9	)	)	-RRB-
10_1101-436634	289	10	.	.	.
10_1101-436634	290	1	The	the	DT
10_1101-436634	290	2	resulting	result	VBG
10_1101-436634	290	3	output	output	NN
10_1101-436634	290	4	is	be	VBZ
10_1101-436634	290	5	then	then	RB
10_1101-436634	290	6	the	the	DT
10_1101-436634	290	7	same	same	JJ
10_1101-436634	290	8	as	as	IN
10_1101-436634	290	9	cis	cis	NN
10_1101-436634	290	10	-	-	HYPH
10_1101-436634	290	11	splice	splice	NN
10_1101-436634	290	12	-	-	HYPH
10_1101-436634	290	13	effects	effect	NNS
10_1101-436634	290	14	identify	identify	VBP
10_1101-436634	290	15	,	,	,
10_1101-436634	290	16	but	but	CC
10_1101-436634	290	17	limited	limit	VBN
10_1101-436634	290	18	to	to	IN
10_1101-436634	290	19	the	the	DT
10_1101-436634	290	20	junctions	junction	NNS
10_1101-436634	290	21	provided	provide	VBN
10_1101-436634	290	22	as	as	IN
10_1101-436634	290	23	input	input	NN
10_1101-436634	290	24	.	.	.
10_1101-436634	291	1	.CC	.CC	NFP
10_1101-436634	291	2	-	-	:
10_1101-436634	291	3	BY	by	IN
10_1101-436634	291	4	-	-	HYPH
10_1101-436634	291	5	NC	NC	NNP
10_1101-436634	291	6	-	-	HYPH
10_1101-436634	291	7	ND	ND	NNP
10_1101-436634	291	8	4.0	4.0	CD
10_1101-436634	291	9	International	international	JJ
10_1101-436634	291	10	licensea	licensea	NNS
10_1101-436634	291	11	certified	certify	VBN
10_1101-436634	291	12	by	by	IN
10_1101-436634	291	13	peer	peer	NN
10_1101-436634	291	14	review	review	NN
10_1101-436634	291	15	)	)	-RRB-
10_1101-436634	291	16	is	be	VBZ
10_1101-436634	291	17	the	the	DT
10_1101-436634	291	18	author	author	NN
10_1101-436634	291	19	/	/	SYM
10_1101-436634	291	20	funder	funder	NN
10_1101-436634	291	21	,	,	,
10_1101-436634	291	22	who	who	WP
10_1101-436634	291	23	has	have	VBZ
10_1101-436634	291	24	granted	grant	VBN
10_1101-436634	291	25	bioRxiv	biorxiv	IN
10_1101-436634	291	26	a	a	DT
10_1101-436634	291	27	license	license	NN
10_1101-436634	291	28	to	to	TO
10_1101-436634	291	29	display	display	VB
10_1101-436634	291	30	the	the	DT
10_1101-436634	291	31	preprint	preprint	NN
10_1101-436634	291	32	in	in	IN
10_1101-436634	291	33	perpetuity	perpetuity	NN
10_1101-436634	291	34	.	.	.
10_1101-436634	292	1	It	-PRON-	PRP
10_1101-436634	292	2	is	be	VBZ
10_1101-436634	292	3	made	make	VBN
10_1101-436634	292	4	available	available	JJ
10_1101-436634	292	5	under	under	IN
10_1101-436634	292	6	The	the	DT
10_1101-436634	292	7	copyright	copyright	NN
10_1101-436634	292	8	holder	holder	NN
10_1101-436634	292	9	for	for	IN
10_1101-436634	292	10	this	this	DT
10_1101-436634	292	11	preprint	preprint	NN
10_1101-436634	292	12	(	(	-LRB-
10_1101-436634	292	13	which	which	WDT
10_1101-436634	292	14	was	be	VBD
10_1101-436634	292	15	notthis	notthis	DT
10_1101-436634	292	16	version	version	NN
10_1101-436634	292	17	posted	post	VBN
10_1101-436634	292	18	January	January	NNP
10_1101-436634	292	19	5	5	CD
10_1101-436634	292	20	,	,	,
10_1101-436634	292	21	2021	2021	CD
10_1101-436634	292	22	.	.	.
10_1101-436634	292	23	;	;	:
10_1101-436634	292	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	292	25	:	:	:
10_1101-436634	292	26	bioRxiv	biorxiv	VB
10_1101-436634	292	27	preprint	preprint	NN
10_1101-436634	292	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	292	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	RB
10_1101-436634	292	30	14	14	CD
10_1101-436634	292	31	Analysis	Analysis	NNP
10_1101-436634	292	32	Dataset	Dataset	NNP
10_1101-436634	292	33	Description	Description	NNP
10_1101-436634	292	34	32	32	CD
10_1101-436634	292	35	cancer	cancer	NN
10_1101-436634	292	36	cohorts	cohort	NNS
10_1101-436634	292	37	were	be	VBD
10_1101-436634	292	38	analyzed	analyze	VBN
10_1101-436634	292	39	from	from	IN
10_1101-436634	292	40	TCGA	TCGA	NNP
10_1101-436634	292	41	.	.	.
10_1101-436634	293	1	These	these	DT
10_1101-436634	293	2	cancer	cancer	NN
10_1101-436634	293	3	types	type	NNS
10_1101-436634	293	4	are	be	VBP
10_1101-436634	293	5	Adrenocortical	adrenocortical	JJ
10_1101-436634	293	6	carcinoma	carcinoma	NN
10_1101-436634	293	7	(	(	-LRB-
10_1101-436634	293	8	ACC	ACC	NNP
10_1101-436634	293	9	)	)	-RRB-
10_1101-436634	293	10	,	,	,
10_1101-436634	293	11	Bladder	Bladder	NNP
10_1101-436634	293	12	Urothelial	Urothelial	NNP
10_1101-436634	293	13	Carcinoma	Carcinoma	NNP
10_1101-436634	293	14	(	(	-LRB-
10_1101-436634	293	15	BLCA	BLCA	NNP
10_1101-436634	293	16	)	)	-RRB-
10_1101-436634	293	17	,	,	,
10_1101-436634	293	18	Brain	Brain	NNP
10_1101-436634	293	19	Lower	low	JJR
10_1101-436634	293	20	Grade	Grade	NNP
10_1101-436634	293	21	Glioma	Glioma	NNP
10_1101-436634	293	22	(	(	-LRB-
10_1101-436634	293	23	LGG	LGG	NNP
10_1101-436634	293	24	)	)	-RRB-
10_1101-436634	293	25	,	,	,
10_1101-436634	293	26	Breast	breast	NN
10_1101-436634	293	27	invasive	invasive	JJ
10_1101-436634	293	28	carcinoma	carcinoma	NN
10_1101-436634	293	29	(	(	-LRB-
10_1101-436634	293	30	BRCA	BRCA	NNP
10_1101-436634	293	31	)	)	-RRB-
10_1101-436634	293	32	,	,	,
10_1101-436634	293	33	Cervical	cervical	JJ
10_1101-436634	293	34	squamous	squamous	JJ
10_1101-436634	293	35	cell	cell	NN
10_1101-436634	293	36	carcinoma	carcinoma	NN
10_1101-436634	293	37	and	and	CC
10_1101-436634	293	38	endocervical	endocervical	JJ
10_1101-436634	293	39	adenocarcinoma	adenocarcinoma	NN
10_1101-436634	293	40	(	(	-LRB-
10_1101-436634	293	41	CESC	CESC	NNP
10_1101-436634	293	42	)	)	-RRB-
10_1101-436634	293	43	,	,	,
10_1101-436634	293	44	Cholangiocarcinoma	Cholangiocarcinoma	NNP
10_1101-436634	293	45	(	(	-LRB-
10_1101-436634	293	46	CHOL	CHOL	NNP
10_1101-436634	293	47	)	)	-RRB-
10_1101-436634	293	48	,	,	,
10_1101-436634	293	49	Colon	colon	NN
10_1101-436634	293	50	adenocarcinoma	adenocarcinoma	NN
10_1101-436634	293	51	(	(	-LRB-
10_1101-436634	293	52	COAD	COAD	NNP
10_1101-436634	293	53	)	)	-RRB-
10_1101-436634	293	54	,	,	,
10_1101-436634	293	55	Esophageal	esophageal	JJ
10_1101-436634	293	56	carcinoma	carcinoma	NN
10_1101-436634	293	57	(	(	-LRB-
10_1101-436634	293	58	ESCA	ESCA	NNP
10_1101-436634	293	59	)	)	-RRB-
10_1101-436634	293	60	,	,	,
10_1101-436634	293	61	Glioblastoma	Glioblastoma	NNP
10_1101-436634	293	62	multiforme	multiforme	NN
10_1101-436634	293	63	(	(	-LRB-
10_1101-436634	293	64	GBM	GBM	NNP
10_1101-436634	293	65	)	)	-RRB-
10_1101-436634	293	66	,	,	,
10_1101-436634	293	67	Head	Head	NNP
10_1101-436634	293	68	and	and	CC
10_1101-436634	293	69	Neck	Neck	NNP
10_1101-436634	293	70	squamous	squamous	JJ
10_1101-436634	293	71	cell	cell	NN
10_1101-436634	293	72	carcinoma	carcinoma	NN
10_1101-436634	293	73	(	(	-LRB-
10_1101-436634	293	74	HNSC	HNSC	NNP
10_1101-436634	293	75	)	)	-RRB-
10_1101-436634	293	76	,	,	,
10_1101-436634	293	77	Kidney	Kidney	NNP
10_1101-436634	293	78	Chromophobe	Chromophobe	NNP
10_1101-436634	293	79	(	(	-LRB-
10_1101-436634	293	80	KICH	KICH	NNP
10_1101-436634	293	81	)	)	-RRB-
10_1101-436634	293	82	,	,	,
10_1101-436634	293	83	Kidney	Kidney	NNP
10_1101-436634	293	84	renal	renal	JJ
10_1101-436634	293	85	clear	clear	JJ
10_1101-436634	293	86	cell	cell	NN
10_1101-436634	293	87	carcinoma	carcinoma	NN
10_1101-436634	293	88	(	(	-LRB-
10_1101-436634	293	89	KIRC	KIRC	NNP
10_1101-436634	293	90	)	)	-RRB-
10_1101-436634	293	91	,	,	,
10_1101-436634	293	92	Kidney	Kidney	NNP
10_1101-436634	293	93	renal	renal	JJ
10_1101-436634	293	94	papillary	papillary	JJ
10_1101-436634	293	95	cell	cell	NN
10_1101-436634	293	96	carcinoma	carcinoma	NN
10_1101-436634	293	97	(	(	-LRB-
10_1101-436634	293	98	KIRP	KIRP	NNP
10_1101-436634	293	99	)	)	-RRB-
10_1101-436634	293	100	,	,	,
10_1101-436634	293	101	Liver	Liver	NNP
10_1101-436634	293	102	hepatocellular	hepatocellular	NN
10_1101-436634	293	103	carcinoma	carcinoma	NN
10_1101-436634	293	104	(	(	-LRB-
10_1101-436634	293	105	LIHC	LIHC	NNP
10_1101-436634	293	106	)	)	-RRB-
10_1101-436634	293	107	,	,	,
10_1101-436634	293	108	Lung	Lung	NNP
10_1101-436634	293	109	adenocarcinoma	adenocarcinoma	NN
10_1101-436634	293	110	(	(	-LRB-
10_1101-436634	293	111	LUAD	luad	RB
10_1101-436634	293	112	)	)	-RRB-
10_1101-436634	293	113	,	,	,
10_1101-436634	293	114	Lung	Lung	NNP
10_1101-436634	293	115	squamous	squamous	JJ
10_1101-436634	293	116	cell	cell	NN
10_1101-436634	293	117	carcinoma	carcinoma	NN
10_1101-436634	293	118	(	(	-LRB-
10_1101-436634	293	119	LUSC	LUSC	NNP
10_1101-436634	293	120	)	)	-RRB-
10_1101-436634	293	121	,	,	,
10_1101-436634	293	122	Lymphoid	Lymphoid	NNP
10_1101-436634	293	123	Neoplasm	Neoplasm	NNP
10_1101-436634	293	124	Diffuse	Diffuse	NNP
10_1101-436634	293	125	Large	large	JJ
10_1101-436634	293	126	B	b	NN
10_1101-436634	293	127	cell	cell	NN
10_1101-436634	293	128	Lymphoma	Lymphoma	NNP
10_1101-436634	293	129	(	(	-LRB-
10_1101-436634	293	130	DLBC	DLBC	NNP
10_1101-436634	293	131	)	)	-RRB-
10_1101-436634	293	132	,	,	,
10_1101-436634	293	133	Mesothelioma	Mesothelioma	NNP
10_1101-436634	293	134	(	(	-LRB-
10_1101-436634	293	135	MESO	MESO	NNP
10_1101-436634	293	136	)	)	-RRB-
10_1101-436634	293	137	,	,	,
10_1101-436634	293	138	Ovarian	ovarian	JJ
10_1101-436634	293	139	serous	serous	JJ
10_1101-436634	293	140	cystadenocarcinoma	cystadenocarcinoma	NN
10_1101-436634	293	141	(	(	-LRB-
10_1101-436634	293	142	OV	OV	NNP
10_1101-436634	293	143	)	)	-RRB-
10_1101-436634	293	144	,	,	,
10_1101-436634	293	145	Pancreatic	pancreatic	JJ
10_1101-436634	293	146	adenocarcinoma	adenocarcinoma	NN
10_1101-436634	293	147	(	(	-LRB-
10_1101-436634	293	148	PAAD	PAAD	NNP
10_1101-436634	293	149	)	)	-RRB-
10_1101-436634	293	150	,	,	,
10_1101-436634	293	151	Pheochromocytoma	Pheochromocytoma	NNP
10_1101-436634	293	152	and	and	CC
10_1101-436634	293	153	Paraganglioma	Paraganglioma	NNP
10_1101-436634	293	154	(	(	-LRB-
10_1101-436634	293	155	PCPG	PCPG	NNP
10_1101-436634	293	156	)	)	-RRB-
10_1101-436634	293	157	,	,	,
10_1101-436634	293	158	Prostate	Prostate	NNP
10_1101-436634	293	159	adenocarcinoma	adenocarcinoma	NN
10_1101-436634	293	160	(	(	-LRB-
10_1101-436634	293	161	PRAD	PRAD	NNP
10_1101-436634	293	162	)	)	-RRB-
10_1101-436634	293	163	,	,	,
10_1101-436634	293	164	Rectum	Rectum	NNP
10_1101-436634	293	165	adenocarcinoma	adenocarcinoma	NN
10_1101-436634	293	166	(	(	-LRB-
10_1101-436634	293	167	READ	READ	NNP
10_1101-436634	293	168	)	)	-RRB-
10_1101-436634	293	169	,	,	,
10_1101-436634	293	170	Sarcoma	Sarcoma	NNP
10_1101-436634	293	171	(	(	-LRB-
10_1101-436634	293	172	SARC	SARC	NNP
10_1101-436634	293	173	)	)	-RRB-
10_1101-436634	293	174	,	,	,
10_1101-436634	293	175	Skin	Skin	NNP
10_1101-436634	293	176	Cutaneous	Cutaneous	NNP
10_1101-436634	293	177	Melanoma	Melanoma	NNP
10_1101-436634	293	178	(	(	-LRB-
10_1101-436634	293	179	SKCM	SKCM	NNP
10_1101-436634	293	180	)	)	-RRB-
10_1101-436634	293	181	,	,	,
10_1101-436634	293	182	Stomach	stomach	NN
10_1101-436634	293	183	adenocarcinoma	adenocarcinoma	NN
10_1101-436634	293	184	(	(	-LRB-
10_1101-436634	293	185	STAD	STAD	NNP
10_1101-436634	293	186	)	)	-RRB-
10_1101-436634	293	187	,	,	,
10_1101-436634	293	188	Testicular	Testicular	NNP
10_1101-436634	293	189	Germ	Germ	NNP
10_1101-436634	293	190	Cell	Cell	NNP
10_1101-436634	293	191	Tumors	Tumors	NNPS
10_1101-436634	293	192	(	(	-LRB-
10_1101-436634	293	193	TGCT	TGCT	NNP
10_1101-436634	293	194	)	)	-RRB-
10_1101-436634	293	195	,	,	,
10_1101-436634	293	196	Thymoma	Thymoma	NNP
10_1101-436634	293	197	(	(	-LRB-
10_1101-436634	293	198	THYM	THYM	NNP
10_1101-436634	293	199	)	)	-RRB-
10_1101-436634	293	200	,	,	,
10_1101-436634	293	201	Thyroid	Thyroid	NNP
10_1101-436634	293	202	carcinoma	carcinoma	NN
10_1101-436634	293	203	(	(	-LRB-
10_1101-436634	293	204	THCA	THCA	NNP
10_1101-436634	293	205	)	)	-RRB-
10_1101-436634	293	206	,	,	,
10_1101-436634	293	207	Uterine	Uterine	NNP
10_1101-436634	293	208	Carcinosarcoma	Carcinosarcoma	NNP
10_1101-436634	293	209	(	(	-LRB-
10_1101-436634	293	210	UCS	UCS	NNP
10_1101-436634	293	211	)	)	-RRB-
10_1101-436634	293	212	,	,	,
10_1101-436634	293	213	Uterine	Uterine	NNP
10_1101-436634	293	214	Corpus	Corpus	NNP
10_1101-436634	293	215	Endometrial	Endometrial	NNP
10_1101-436634	293	216	Carcinoma	Carcinoma	NNP
10_1101-436634	293	217	(	(	-LRB-
10_1101-436634	293	218	UCEC	UCEC	NNP
10_1101-436634	293	219	)	)	-RRB-
10_1101-436634	293	220	,	,	,
10_1101-436634	293	221	and	and	CC
10_1101-436634	293	222	Uveal	Uveal	NNP
10_1101-436634	293	223	Melanoma	Melanoma	NNP
10_1101-436634	293	224	(	(	-LRB-
10_1101-436634	293	225	UVM	UVM	NNP
10_1101-436634	293	226	)	)	-RRB-
10_1101-436634	293	227	.	.	.
10_1101-436634	294	1	Three	three	CD
10_1101-436634	294	2	cohorts	cohort	NNS
10_1101-436634	294	3	were	be	VBD
10_1101-436634	294	4	derived	derive	VBN
10_1101-436634	294	5	from	from	IN
10_1101-436634	294	6	patients	patient	NNS
10_1101-436634	294	7	at	at	IN
10_1101-436634	294	8	Washington	Washington	NNP
10_1101-436634	294	9	University	University	NNP
10_1101-436634	294	10	in	in	IN
10_1101-436634	294	11	St.	St.	NNP
10_1101-436634	294	12	Louis	Louis	NNP
10_1101-436634	294	13	.	.	.
10_1101-436634	295	1	These	these	DT
10_1101-436634	295	2	cohorts	cohort	NNS
10_1101-436634	295	3	are	be	VBP
10_1101-436634	295	4	Hepatocellular	Hepatocellular	NNP
10_1101-436634	295	5	Carcinoma	Carcinoma	NNP
10_1101-436634	295	6	(	(	-LRB-
10_1101-436634	295	7	HCC	HCC	NNP
10_1101-436634	295	8	)	)	-RRB-
10_1101-436634	295	9	,	,	,
10_1101-436634	295	10	Oral	Oral	NNP
10_1101-436634	295	11	Squamous	Squamous	NNP
10_1101-436634	295	12	Cell	Cell	NNP
10_1101-436634	295	13	Carcinoma	Carcinoma	NNP
10_1101-436634	295	14	(	(	-LRB-
10_1101-436634	295	15	OSCC	OSCC	NNP
10_1101-436634	295	16	)	)	-RRB-
10_1101-436634	295	17	,	,	,
10_1101-436634	295	18	and	and	CC
10_1101-436634	295	19	Small	Small	NNP
10_1101-436634	295	20	Cell	Cell	NNP
10_1101-436634	295	21	Lung	Lung	NNP
10_1101-436634	295	22	Cancer	Cancer	NNP
10_1101-436634	295	23	(	(	-LRB-
10_1101-436634	295	24	SCLC	SCLC	NNP
10_1101-436634	295	25	)	)	-RRB-
10_1101-436634	295	26	.	.	.
10_1101-436634	296	1	Sample	sample	NN
10_1101-436634	296	2	processing	processing	NN
10_1101-436634	296	3	We	-PRON-	PRP
10_1101-436634	296	4	applied	apply	VBD
10_1101-436634	296	5	RegTools	regtool	NNS
10_1101-436634	296	6	to	to	TO
10_1101-436634	296	7	35	35	CD
10_1101-436634	296	8	tumor	tumor	NN
10_1101-436634	296	9	cohorts	cohort	NNS
10_1101-436634	296	10	.	.	.
10_1101-436634	297	1	Genomic	genomic	JJ
10_1101-436634	297	2	and	and	CC
10_1101-436634	297	3	transcriptomic	transcriptomic	JJ
10_1101-436634	297	4	data	datum	NNS
10_1101-436634	297	5	for	for	IN
10_1101-436634	297	6	32	32	CD
10_1101-436634	297	7	cohorts	cohort	NNS
10_1101-436634	297	8	were	be	VBD
10_1101-436634	297	9	obtained	obtain	VBN
10_1101-436634	297	10	from	from	IN
10_1101-436634	297	11	The	the	DT
10_1101-436634	297	12	Cancer	Cancer	NNP
10_1101-436634	297	13	Genome	Genome	NNP
10_1101-436634	297	14	Atlas	Atlas	NNP
10_1101-436634	297	15	(	(	-LRB-
10_1101-436634	297	16	TCGA	TCGA	NNP
10_1101-436634	297	17	)	)	-RRB-
10_1101-436634	297	18	.	.	.
10_1101-436634	298	1	Information	information	NN
10_1101-436634	298	2	regarding	regard	VBG
10_1101-436634	298	3	the	the	DT
10_1101-436634	298	4	alignment	alignment	NN
10_1101-436634	298	5	and	and	CC
10_1101-436634	298	6	variant	variant	JJ
10_1101-436634	298	7	calling	calling	NN
10_1101-436634	298	8	for	for	IN
10_1101-436634	298	9	these	these	DT
10_1101-436634	298	10	samples	sample	NNS
10_1101-436634	298	11	is	be	VBZ
10_1101-436634	298	12	described	describe	VBN
10_1101-436634	298	13	by	by	IN
10_1101-436634	298	14	the	the	DT
10_1101-436634	298	15	Genomic	Genomic	NNP
10_1101-436634	298	16	Data	Data	NNP
10_1101-436634	298	17	Commons	Commons	NNP
10_1101-436634	298	18	data	data	NN
10_1101-436634	298	19	harmonization	harmonization	NN
10_1101-436634	298	20	effort47	effort47	NNS
10_1101-436634	298	21	.	.	.
10_1101-436634	299	1	Whole	whole	JJ
10_1101-436634	299	2	exome	exome	JJ
10_1101-436634	299	3	sequencing	sequencing	NN
10_1101-436634	299	4	(	(	-LRB-
10_1101-436634	299	5	WES	WES	NNP
10_1101-436634	299	6	)	)	-RRB-
10_1101-436634	299	7	mutation	mutation	NN
10_1101-436634	299	8	calls	call	NNS
10_1101-436634	299	9	for	for	IN
10_1101-436634	299	10	these	these	DT
10_1101-436634	299	11	samples	sample	NNS
10_1101-436634	299	12	from	from	IN
10_1101-436634	299	13	MuSE48	muse48	NN
10_1101-436634	299	14	,	,	,
10_1101-436634	299	15	MuTect249	mutect249	NN
10_1101-436634	299	16	,	,	,
10_1101-436634	299	17	VarScan250	VarScan250	NNP
10_1101-436634	299	18	,	,	,
10_1101-436634	299	19	and	and	CC
10_1101-436634	299	20	SomaticSniper51	somaticsniper51	NN
10_1101-436634	299	21	,	,	,
10_1101-436634	299	22	were	be	VBD
10_1101-436634	299	23	left	leave	VBN
10_1101-436634	299	24	-	-	HYPH
10_1101-436634	299	25	aligned	align	VBN
10_1101-436634	299	26	,	,	,
10_1101-436634	299	27	trimmed	trim	VBN
10_1101-436634	299	28	,	,	,
10_1101-436634	299	29	and	and	CC
10_1101-436634	299	30	decomposed	decompose	VBD
10_1101-436634	299	31	to	to	TO
10_1101-436634	299	32	ensure	ensure	VB
10_1101-436634	299	33	the	the	DT
10_1101-436634	299	34	correct	correct	JJ
10_1101-436634	299	35	representation	representation	NN
10_1101-436634	299	36	of	of	IN
10_1101-436634	299	37	the	the	DT
10_1101-436634	299	38	variants	variant	NNS
10_1101-436634	299	39	across	across	IN
10_1101-436634	299	40	the	the	DT
10_1101-436634	299	41	multiple	multiple	JJ
10_1101-436634	299	42	callers	caller	NNS
10_1101-436634	299	43	.	.	.
10_1101-436634	300	1	Samples	sample	NNS
10_1101-436634	300	2	for	for	IN
10_1101-436634	300	3	the	the	DT
10_1101-436634	300	4	remaining	remain	VBG
10_1101-436634	300	5	three	three	CD
10_1101-436634	300	6	cohorts	cohort	NNS
10_1101-436634	300	7	,	,	,
10_1101-436634	300	8	HCC	HCC	NNP
10_1101-436634	300	9	,	,	,
10_1101-436634	300	10	SCLC	SCLC	NNP
10_1101-436634	300	11	,	,	,
10_1101-436634	300	12	and	and	CC
10_1101-436634	300	13	OSCC	OSCC	NNP
10_1101-436634	300	14	,	,	,
10_1101-436634	300	15	were	be	VBD
10_1101-436634	300	16	sequenced	sequence	VBN
10_1101-436634	300	17	at	at	IN
10_1101-436634	300	18	Washington	Washington	NNP
10_1101-436634	300	19	University	University	NNP
10_1101-436634	300	20	in	in	IN
10_1101-436634	300	21	St.	St.	NNP
10_1101-436634	300	22	Louis	Louis	NNP
10_1101-436634	300	23	.	.	.
10_1101-436634	301	1	Genomic	genomic	JJ
10_1101-436634	301	2	data	datum	NNS
10_1101-436634	301	3	were	be	VBD
10_1101-436634	301	4	produced	produce	VBN
10_1101-436634	301	5	by	by	IN
10_1101-436634	301	6	WES	WES	NNP
10_1101-436634	301	7	for	for	IN
10_1101-436634	301	8	SCLC	SCLC	NNP
10_1101-436634	301	9	and	and	CC
10_1101-436634	301	10	OSCC	OSCC	NNP
10_1101-436634	301	11	and	and	CC
10_1101-436634	301	12	whole	whole	JJ
10_1101-436634	301	13	genome	genome	JJ
10_1101-436634	301	14	sequencing	sequencing	NN
10_1101-436634	301	15	(	(	-LRB-
10_1101-436634	301	16	WGS	WGS	NNP
10_1101-436634	301	17	)	)	-RRB-
10_1101-436634	301	18	for	for	IN
10_1101-436634	301	19	HCC	HCC	NNP
10_1101-436634	301	20	.	.	.
10_1101-436634	302	1	Normal	normal	JJ
10_1101-436634	302	2	genomic	genomic	JJ
10_1101-436634	302	3	data	datum	NNS
10_1101-436634	302	4	of	of	IN
10_1101-436634	302	5	the	the	DT
10_1101-436634	302	6	same	same	JJ
10_1101-436634	302	7	sequencing	sequencing	NN
10_1101-436634	302	8	type	type	NN
10_1101-436634	302	9	and	and	CC
10_1101-436634	302	10	tumor	tumor	NN
10_1101-436634	302	11	RNA	RNA	NNP
10_1101-436634	302	12	-	-	HYPH
10_1101-436634	302	13	seq	seq	NN
10_1101-436634	302	14	data	datum	NNS
10_1101-436634	302	15	were	be	VBD
10_1101-436634	302	16	also	also	RB
10_1101-436634	302	17	available	available	JJ
10_1101-436634	302	18	for	for	IN
10_1101-436634	302	19	all	all	DT
10_1101-436634	302	20	subjects	subject	NNS
10_1101-436634	302	21	.	.	.
10_1101-436634	303	1	Sequence	sequence	NN
10_1101-436634	303	2	data	datum	NNS
10_1101-436634	303	3	were	be	VBD
10_1101-436634	303	4	aligned	align	VBN
10_1101-436634	303	5	using	use	VBG
10_1101-436634	303	6	the	the	DT
10_1101-436634	303	7	Genome	Genome	NNP
10_1101-436634	303	8	Modeling	Modeling	NNP
10_1101-436634	303	9	System	System	NNP
10_1101-436634	303	10	(	(	-LRB-
10_1101-436634	303	11	GMS)52	GMS)52	NNP
10_1101-436634	303	12	using	use	VBG
10_1101-436634	303	13	TopHat2	TopHat2	NNP
10_1101-436634	303	14	for	for	IN
10_1101-436634	303	15	RNA	RNA	NNP
10_1101-436634	303	16	and	and	CC
10_1101-436634	303	17	BWA	BWA	NNP
10_1101-436634	303	18	-	-	HYPH
10_1101-436634	303	19	MEM53	MEM53	NNP
10_1101-436634	303	20	for	for	IN
10_1101-436634	303	21	DNA	DNA	NNP
10_1101-436634	303	22	.	.	.
10_1101-436634	304	1	HCC	HCC	NNP
10_1101-436634	304	2	and	and	CC
10_1101-436634	304	3	SCLC	SCLC	NNP
10_1101-436634	304	4	were	be	VBD
10_1101-436634	304	5	aligned	align	VBN
10_1101-436634	304	6	to	to	IN
10_1101-436634	304	7	GRCh37	GRCh37	NNP
10_1101-436634	304	8	while	while	IN
10_1101-436634	304	9	OSCC	OSCC	NNP
10_1101-436634	304	10	was	be	VBD
10_1101-436634	304	11	aligned	align	VBN
10_1101-436634	304	12	to	to	IN
10_1101-436634	304	13	GRCh38	GRCh38	NNP
10_1101-436634	304	14	.	.	.
10_1101-436634	305	1	Somatic	somatic	JJ
10_1101-436634	305	2	variant	variant	JJ
10_1101-436634	305	3	calls	call	NNS
10_1101-436634	305	4	were	be	VBD
10_1101-436634	305	5	made	make	VBN
10_1101-436634	305	6	using	use	VBG
10_1101-436634	305	7	Samtools	Samtools	NNP
10_1101-436634	305	8	v0.1.126	v0.1.126	NN
10_1101-436634	305	9	,	,	,
10_1101-436634	305	10	SomaticSniper2	somaticsniper2	CD
10_1101-436634	305	11	v1.0.251	v1.0.251	NNS
10_1101-436634	305	12	,	,	,
10_1101-436634	305	13	Strelka	Strelka	NNP
10_1101-436634	305	14	V0.4.6.254	V0.4.6.254	NNS
10_1101-436634	305	15	,	,	,
10_1101-436634	305	16	and	and	CC
10_1101-436634	305	17	VarScan	VarScan	NNP
10_1101-436634	305	18	v2.2.650,54	v2.2.650,54	NNP
10_1101-436634	305	19	through	through	IN
10_1101-436634	305	20	the	the	DT
10_1101-436634	305	21	GMS	GMS	NNP
10_1101-436634	305	22	.	.	.
10_1101-436634	306	1	High	high	JJ
10_1101-436634	306	2	-	-	HYPH
10_1101-436634	306	3	quality	quality	NN
10_1101-436634	306	4	mutations	mutation	NNS
10_1101-436634	306	5	for	for	IN
10_1101-436634	306	6	all	all	DT
10_1101-436634	306	7	samples	sample	NNS
10_1101-436634	306	8	were	be	VBD
10_1101-436634	306	9	then	then	RB
10_1101-436634	306	10	selected	select	VBN
10_1101-436634	306	11	by	by	IN
10_1101-436634	306	12	requiring	require	VBG
10_1101-436634	306	13	that	that	IN
10_1101-436634	306	14	a	a	DT
10_1101-436634	306	15	variant	variant	JJ
10_1101-436634	306	16	be	be	NN
10_1101-436634	306	17	called	call	VBN
10_1101-436634	306	18	by	by	IN
10_1101-436634	306	19	two	two	CD
10_1101-436634	306	20	of	of	IN
10_1101-436634	306	21	the	the	DT
10_1101-436634	306	22	four	four	CD
10_1101-436634	306	23	variant	variant	JJ
10_1101-436634	306	24	callers	caller	NNS
10_1101-436634	306	25	.	.	.
10_1101-436634	307	1	Candidate	candidate	NN
10_1101-436634	307	2	junction	junction	NN
10_1101-436634	307	3	filtering	filter	VBG
10_1101-436634	307	4	To	to	TO
10_1101-436634	307	5	generate	generate	VB
10_1101-436634	307	6	results	result	NNS
10_1101-436634	307	7	for	for	IN
10_1101-436634	307	8	4	4	CD
10_1101-436634	307	9	splice	splice	NN
10_1101-436634	307	10	variant	variant	JJ
10_1101-436634	307	11	window	window	NN
10_1101-436634	307	12	sizes	size	NNS
10_1101-436634	307	13	,	,	,
10_1101-436634	307	14	we	-PRON-	PRP
10_1101-436634	307	15	ran	run	VBD
10_1101-436634	307	16	cis	cis	NN
10_1101-436634	307	17	-	-	HYPH
10_1101-436634	307	18	splice	splice	NN
10_1101-436634	307	19	-	-	HYPH
10_1101-436634	307	20	effects	effect	NNS
10_1101-436634	307	21	identify	identify	VBP
10_1101-436634	307	22	with	with	IN
10_1101-436634	307	23	4	4	CD
10_1101-436634	307	24	sets	set	NNS
10_1101-436634	307	25	of	of	IN
10_1101-436634	307	26	splice	splice	NN
10_1101-436634	307	27	variant	variant	JJ
10_1101-436634	307	28	window	window	NN
10_1101-436634	307	29	parameters	parameter	NNS
10_1101-436634	307	30	.	.	.
10_1101-436634	308	1	For	for	IN
10_1101-436634	308	2	our	-PRON-	PRP$
10_1101-436634	308	3	“	"	``
10_1101-436634	308	4	i2e3	i2e3	NNP
10_1101-436634	308	5	”	"	''
10_1101-436634	308	6	window	window	NN
10_1101-436634	308	7	(	(	-LRB-
10_1101-436634	308	8	RegTools	RegTools	NNP
10_1101-436634	308	9	default	default	NN
10_1101-436634	308	10	)	)	-RRB-
10_1101-436634	308	11	,	,	,
10_1101-436634	308	12	to	to	TO
10_1101-436634	308	13	examine	examine	VB
10_1101-436634	308	14	intronic	intronic	JJ
10_1101-436634	308	15	variants	variant	NNS
10_1101-436634	308	16	within	within	IN
10_1101-436634	308	17	2	2	CD
10_1101-436634	308	18	bases	basis	NNS
10_1101-436634	308	19	and	and	CC
10_1101-436634	308	20	exonic	exonic	JJ
10_1101-436634	308	21	variants	variant	NNS
10_1101-436634	308	22	within	within	IN
10_1101-436634	308	23	3	3	CD
10_1101-436634	308	24	bases	basis	NNS
10_1101-436634	308	25	of	of	IN
10_1101-436634	308	26	the	the	DT
10_1101-436634	308	27	exon	exon	JJ
10_1101-436634	308	28	edge	edge	NN
10_1101-436634	308	29	,	,	,
10_1101-436634	308	30	we	-PRON-	PRP
10_1101-436634	308	31	set	set	VBP
10_1101-436634	308	32	“	"	``
10_1101-436634	308	33	-i	-i	:
10_1101-436634	308	34	2	2	CD
10_1101-436634	308	35	-e	-e	SYM
10_1101-436634	308	36	3	3	CD
10_1101-436634	308	37	”	"	''
10_1101-436634	308	38	.	.	.
10_1101-436634	309	1	Similarly	similarly	RB
10_1101-436634	309	2	,	,	,
10_1101-436634	309	3	for	for	IN
10_1101-436634	309	4	“	"	``
10_1101-436634	309	5	i50e5	i50e5	NNP
10_1101-436634	309	6	”	"	''
10_1101-436634	309	7	,	,	,
10_1101-436634	309	8	to	to	TO
10_1101-436634	309	9	examine	examine	VB
10_1101-436634	309	10	intronic	intronic	JJ
10_1101-436634	309	11	variants	variant	NNS
10_1101-436634	309	12	within	within	IN
10_1101-436634	309	13	50	50	CD
10_1101-436634	309	14	bases	basis	NNS
10_1101-436634	309	15	and	and	CC
10_1101-436634	309	16	exonic	exonic	JJ
10_1101-436634	309	17	variants	variant	NNS
10_1101-436634	309	18	within	within	IN
10_1101-436634	309	19	5	5	CD
10_1101-436634	309	20	bases	basis	NNS
10_1101-436634	309	21	of	of	IN
10_1101-436634	309	22	the	the	DT
10_1101-436634	309	23	exon	exon	JJ
10_1101-436634	309	24	edge	edge	NN
10_1101-436634	309	25	,	,	,
10_1101-436634	309	26	we	-PRON-	PRP
10_1101-436634	309	27	set	set	VBP
10_1101-436634	309	28	“	"	``
10_1101-436634	309	29	-i	-i	:
10_1101-436634	309	30	50	50	CD
10_1101-436634	309	31	-e	-e	SYM
10_1101-436634	309	32	5	5	CD
10_1101-436634	309	33	”	"	''
10_1101-436634	309	34	.	.	.
10_1101-436634	310	1	To	to	TO
10_1101-436634	310	2	view	view	VB
10_1101-436634	310	3	all	all	DT
10_1101-436634	310	4	exonic	exonic	JJ
10_1101-436634	310	5	variants	variant	NNS
10_1101-436634	310	6	,	,	,
10_1101-436634	310	7	we	-PRON-	PRP
10_1101-436634	310	8	simply	simply	RB
10_1101-436634	310	9	set	set	VBP
10_1101-436634	310	10	“	"	``
10_1101-436634	310	11	-	-	HYPH
10_1101-436634	310	12	.CC	.CC	:
10_1101-436634	310	13	-	-	HYPH
10_1101-436634	310	14	BY	by	IN
10_1101-436634	310	15	-	-	HYPH
10_1101-436634	310	16	NC	NC	NNP
10_1101-436634	310	17	-	-	HYPH
10_1101-436634	310	18	ND	ND	NNP
10_1101-436634	310	19	4.0	4.0	CD
10_1101-436634	310	20	International	international	JJ
10_1101-436634	310	21	licensea	licensea	NNS
10_1101-436634	310	22	certified	certify	VBN
10_1101-436634	310	23	by	by	IN
10_1101-436634	310	24	peer	peer	NN
10_1101-436634	310	25	review	review	NN
10_1101-436634	310	26	)	)	-RRB-
10_1101-436634	310	27	is	be	VBZ
10_1101-436634	310	28	the	the	DT
10_1101-436634	310	29	author	author	NN
10_1101-436634	310	30	/	/	SYM
10_1101-436634	310	31	funder	funder	NN
10_1101-436634	310	32	,	,	,
10_1101-436634	310	33	who	who	WP
10_1101-436634	310	34	has	have	VBZ
10_1101-436634	310	35	granted	grant	VBN
10_1101-436634	310	36	bioRxiv	biorxiv	IN
10_1101-436634	310	37	a	a	DT
10_1101-436634	310	38	license	license	NN
10_1101-436634	310	39	to	to	TO
10_1101-436634	310	40	display	display	VB
10_1101-436634	310	41	the	the	DT
10_1101-436634	310	42	preprint	preprint	NN
10_1101-436634	310	43	in	in	IN
10_1101-436634	310	44	perpetuity	perpetuity	NN
10_1101-436634	310	45	.	.	.
10_1101-436634	311	1	It	-PRON-	PRP
10_1101-436634	311	2	is	be	VBZ
10_1101-436634	311	3	made	make	VBN
10_1101-436634	311	4	available	available	JJ
10_1101-436634	311	5	under	under	IN
10_1101-436634	311	6	The	the	DT
10_1101-436634	311	7	copyright	copyright	NN
10_1101-436634	311	8	holder	holder	NN
10_1101-436634	311	9	for	for	IN
10_1101-436634	311	10	this	this	DT
10_1101-436634	311	11	preprint	preprint	NN
10_1101-436634	311	12	(	(	-LRB-
10_1101-436634	311	13	which	which	WDT
10_1101-436634	311	14	was	be	VBD
10_1101-436634	311	15	notthis	notthis	DT
10_1101-436634	311	16	version	version	NN
10_1101-436634	311	17	posted	post	VBN
10_1101-436634	311	18	January	January	NNP
10_1101-436634	311	19	5	5	CD
10_1101-436634	311	20	,	,	,
10_1101-436634	311	21	2021	2021	CD
10_1101-436634	311	22	.	.	.
10_1101-436634	311	23	;	;	:
10_1101-436634	311	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	311	25	:	:	:
10_1101-436634	311	26	bioRxiv	biorxiv	VB
10_1101-436634	311	27	preprint	preprint	NN
10_1101-436634	311	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	311	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	CD
10_1101-436634	311	30	15	15	CD
10_1101-436634	311	31	E	e	NN
10_1101-436634	311	32	”	"	''
10_1101-436634	311	33	,	,	,
10_1101-436634	311	34	without	without	IN
10_1101-436634	311	35	“	"	``
10_1101-436634	311	36	-i	-i	:
10_1101-436634	311	37	”	"	''
10_1101-436634	311	38	or	or	CC
10_1101-436634	311	39	“	"	``
10_1101-436634	311	40	-e	-e	:
10_1101-436634	311	41	”	"	''
10_1101-436634	311	42	options	option	NNS
10_1101-436634	311	43	.	.	.
10_1101-436634	312	1	To	to	TO
10_1101-436634	312	2	view	view	VB
10_1101-436634	312	3	all	all	DT
10_1101-436634	312	4	intronic	intronic	JJ
10_1101-436634	312	5	variants	variant	NNS
10_1101-436634	312	6	,	,	,
10_1101-436634	312	7	we	-PRON-	PRP
10_1101-436634	312	8	simply	simply	RB
10_1101-436634	312	9	set	set	VBP
10_1101-436634	312	10	“	"	``
10_1101-436634	312	11	-I	-i	FW
10_1101-436634	312	12	”	"	''
10_1101-436634	312	13	,	,	,
10_1101-436634	312	14	without	without	IN
10_1101-436634	312	15	“	"	``
10_1101-436634	312	16	-i	-i	:
10_1101-436634	312	17	”	"	''
10_1101-436634	312	18	or	or	CC
10_1101-436634	312	19	“	"	``
10_1101-436634	312	20	-e	-e	:
10_1101-436634	312	21	”	"	''
10_1101-436634	312	22	options	option	NNS
10_1101-436634	312	23	.	.	.
10_1101-436634	313	1	TCGA	tcga	NN
10_1101-436634	313	2	samples	sample	NNS
10_1101-436634	313	3	were	be	VBD
10_1101-436634	313	4	processed	process	VBN
10_1101-436634	313	5	with	with	IN
10_1101-436634	313	6	GRCh38.d1.vd1.fa	GRCh38.d1.vd1.fa	HYPH
10_1101-436634	313	7	(	(	-LRB-
10_1101-436634	313	8	downloaded	download	VBN
10_1101-436634	313	9	from	from	IN
10_1101-436634	313	10	the	the	DT
10_1101-436634	313	11	GDC	GDC	NNP
10_1101-436634	313	12	reference	reference	NN
10_1101-436634	313	13	file	file	NN
10_1101-436634	313	14	page	page	NN
10_1101-436634	313	15	at	at	IN
10_1101-436634	313	16	https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-	https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-	NN
10_1101-436634	313	17	files	file	NNS
10_1101-436634	313	18	)	)	-RRB-
10_1101-436634	313	19	as	as	IN
10_1101-436634	313	20	the	the	DT
10_1101-436634	313	21	reference	reference	NN
10_1101-436634	313	22	fasta	fasta	VBZ
10_1101-436634	313	23	file	file	NN
10_1101-436634	313	24	and	and	CC
10_1101-436634	313	25	gencode.v29.annotation.gtf	gencode.v29.annotation.gtf	NNP
10_1101-436634	313	26	(	(	-LRB-
10_1101-436634	313	27	downloaded	download	VBN
10_1101-436634	313	28	via	via	IN
10_1101-436634	313	29	the	the	DT
10_1101-436634	313	30	GENCODE	GENCODE	NNP
10_1101-436634	313	31	FTP	FTP	NNP
10_1101-436634	313	32	)	)	-RRB-
10_1101-436634	313	33	as	as	IN
10_1101-436634	313	34	the	the	DT
10_1101-436634	313	35	reference	reference	NN
10_1101-436634	313	36	transcriptome	transcriptome	VBP
10_1101-436634	313	37	.	.	.
10_1101-436634	314	1	OSCC	OSCC	NNP
10_1101-436634	314	2	was	be	VBD
10_1101-436634	314	3	processed	process	VBN
10_1101-436634	314	4	with	with	IN
10_1101-436634	314	5	Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa	Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa	NNP
10_1101-436634	314	6	and	and	CC
10_1101-436634	314	7	Homo_sapiens.GRCh38.79.gtf	Homo_sapiens.GRCh38.79.gtf	NNS
10_1101-436634	314	8	(	(	-LRB-
10_1101-436634	314	9	both	both	DT
10_1101-436634	314	10	downloaded	download	VBN
10_1101-436634	314	11	from	from	IN
10_1101-436634	314	12	Ensembl	Ensembl	NNP
10_1101-436634	314	13	)	)	-RRB-
10_1101-436634	314	14	.	.	.
10_1101-436634	315	1	HCC	HCC	NNP
10_1101-436634	315	2	and	and	CC
10_1101-436634	315	3	SCLC	SCLC	NNP
10_1101-436634	315	4	were	be	VBD
10_1101-436634	315	5	processed	process	VBN
10_1101-436634	315	6	with	with	IN
10_1101-436634	315	7	Homo_sapiens.GRCh37.dna_sm.primary_assembly.fa	Homo_sapiens.GRCh37.dna_sm.primary_assembly.fa	NNP
10_1101-436634	315	8	and	and	CC
10_1101-436634	315	9	Homo_sapiens.GRCh37.87.gtf	Homo_sapiens.GRCh37.87.gtf	NNP
10_1101-436634	315	10	(	(	-LRB-
10_1101-436634	315	11	both	both	DT
10_1101-436634	315	12	downloaded	download	VBN
10_1101-436634	315	13	from	from	IN
10_1101-436634	315	14	Ensembl	Ensembl	NNP
10_1101-436634	315	15	)	)	-RRB-
10_1101-436634	315	16	.	.	.
10_1101-436634	316	1	Statistical	statistical	JJ
10_1101-436634	316	2	filtering	filtering	NN
10_1101-436634	316	3	of	of	IN
10_1101-436634	316	4	candidate	candidate	NN
10_1101-436634	316	5	events	event	NNS
10_1101-436634	316	6	We	-PRON-	PRP
10_1101-436634	316	7	refer	refer	VBP
10_1101-436634	316	8	to	to	IN
10_1101-436634	316	9	a	a	DT
10_1101-436634	316	10	statistical	statistical	JJ
10_1101-436634	316	11	association	association	NN
10_1101-436634	316	12	between	between	IN
10_1101-436634	316	13	a	a	DT
10_1101-436634	316	14	variant	variant	NN
10_1101-436634	316	15	and	and	CC
10_1101-436634	316	16	a	a	DT
10_1101-436634	316	17	junction	junction	NN
10_1101-436634	316	18	as	as	IN
10_1101-436634	316	19	an	an	DT
10_1101-436634	316	20	“	"	``
10_1101-436634	316	21	event	event	NN
10_1101-436634	316	22	”	"	''
10_1101-436634	316	23	.	.	.
10_1101-436634	317	1	For	for	IN
10_1101-436634	317	2	each	each	DT
10_1101-436634	317	3	event	event	NN
10_1101-436634	317	4	identified	identify	VBN
10_1101-436634	317	5	by	by	IN
10_1101-436634	317	6	RegTools	RegTools	NNP
10_1101-436634	317	7	,	,	,
10_1101-436634	317	8	a	a	DT
10_1101-436634	317	9	normalized	normalized	JJ
10_1101-436634	317	10	score	score	NN
10_1101-436634	317	11	(	(	-LRB-
10_1101-436634	317	12	norm_score	norm_score	NNP
10_1101-436634	317	13	)	)	-RRB-
10_1101-436634	317	14	was	be	VBD
10_1101-436634	317	15	calculated	calculate	VBN
10_1101-436634	317	16	for	for	IN
10_1101-436634	317	17	the	the	DT
10_1101-436634	317	18	junction	junction	NN
10_1101-436634	317	19	of	of	IN
10_1101-436634	317	20	the	the	DT
10_1101-436634	317	21	event	event	NN
10_1101-436634	317	22	by	by	IN
10_1101-436634	317	23	dividing	divide	VBG
10_1101-436634	317	24	the	the	DT
10_1101-436634	317	25	number	number	NN
10_1101-436634	317	26	of	of	IN
10_1101-436634	317	27	reads	read	NNS
10_1101-436634	317	28	supporting	support	VBG
10_1101-436634	317	29	that	that	DT
10_1101-436634	317	30	junction	junction	NN
10_1101-436634	317	31	by	by	IN
10_1101-436634	317	32	the	the	DT
10_1101-436634	317	33	sum	sum	NN
10_1101-436634	317	34	of	of	IN
10_1101-436634	317	35	all	all	DT
10_1101-436634	317	36	reads	read	NNS
10_1101-436634	317	37	for	for	IN
10_1101-436634	317	38	all	all	DT
10_1101-436634	317	39	junctions	junction	NNS
10_1101-436634	317	40	within	within	IN
10_1101-436634	317	41	the	the	DT
10_1101-436634	317	42	splice	splice	NN
10_1101-436634	317	43	junction	junction	NN
10_1101-436634	317	44	region	region	NN
10_1101-436634	317	45	for	for	IN
10_1101-436634	317	46	the	the	DT
10_1101-436634	317	47	variant	variant	NN
10_1101-436634	317	48	of	of	IN
10_1101-436634	317	49	interest	interest	NN
10_1101-436634	317	50	.	.	.
10_1101-436634	318	1	This	this	DT
10_1101-436634	318	2	metric	metric	NN
10_1101-436634	318	3	is	be	VBZ
10_1101-436634	318	4	conceptually	conceptually	RB
10_1101-436634	318	5	similar	similar	JJ
10_1101-436634	318	6	to	to	IN
10_1101-436634	318	7	a	a	DT
10_1101-436634	318	8	“	"	``
10_1101-436634	318	9	percent	percent	NN
10_1101-436634	318	10	-	-	HYPH
10_1101-436634	318	11	spliced	spliced	JJ
10_1101-436634	318	12	in	in	IN
10_1101-436634	318	13	”	"	''
10_1101-436634	318	14	(	(	-LRB-
10_1101-436634	318	15	PSI	PSI	NNP
10_1101-436634	318	16	)	)	-RRB-
10_1101-436634	318	17	index	index	NN
10_1101-436634	318	18	,	,	,
10_1101-436634	318	19	but	but	CC
10_1101-436634	318	20	measures	measure	VBZ
10_1101-436634	318	21	the	the	DT
10_1101-436634	318	22	presence	presence	NN
10_1101-436634	318	23	of	of	IN
10_1101-436634	318	24	entire	entire	JJ
10_1101-436634	318	25	exon	exon	NN
10_1101-436634	318	26	-	-	HYPH
10_1101-436634	318	27	exon	exon	NN
10_1101-436634	318	28	junctions	junction	NNS
10_1101-436634	318	29	,	,	,
10_1101-436634	318	30	instead	instead	RB
10_1101-436634	318	31	of	of	IN
10_1101-436634	318	32	just	just	RB
10_1101-436634	318	33	the	the	DT
10_1101-436634	318	34	inclusion	inclusion	NN
10_1101-436634	318	35	of	of	IN
10_1101-436634	318	36	individual	individual	JJ
10_1101-436634	318	37	exons	exon	NNS
10_1101-436634	318	38	.	.	.
10_1101-436634	319	1	If	if	IN
10_1101-436634	319	2	there	there	EX
10_1101-436634	319	3	were	be	VBD
10_1101-436634	319	4	multiple	multiple	JJ
10_1101-436634	319	5	samples	sample	NNS
10_1101-436634	319	6	that	that	WDT
10_1101-436634	319	7	contained	contain	VBD
10_1101-436634	319	8	the	the	DT
10_1101-436634	319	9	variant	variant	NN
10_1101-436634	319	10	for	for	IN
10_1101-436634	319	11	the	the	DT
10_1101-436634	319	12	event	event	NN
10_1101-436634	319	13	,	,	,
10_1101-436634	319	14	then	then	RB
10_1101-436634	319	15	the	the	DT
10_1101-436634	319	16	mean	mean	NN
10_1101-436634	319	17	of	of	IN
10_1101-436634	319	18	the	the	DT
10_1101-436634	319	19	normalized	normalized	JJ
10_1101-436634	319	20	scores	score	NNS
10_1101-436634	319	21	for	for	IN
10_1101-436634	319	22	the	the	DT
10_1101-436634	319	23	samples	sample	NNS
10_1101-436634	319	24	was	be	VBD
10_1101-436634	319	25	computed	compute	VBN
10_1101-436634	319	26	(	(	-LRB-
10_1101-436634	319	27	mean_norm_score	mean_norm_score	NN
10_1101-436634	319	28	)	)	-RRB-
10_1101-436634	319	29	.	.	.
10_1101-436634	320	1	If	if	IN
10_1101-436634	320	2	only	only	RB
10_1101-436634	320	3	one	one	CD
10_1101-436634	320	4	sample	sample	NN
10_1101-436634	320	5	contained	contain	VBD
10_1101-436634	320	6	the	the	DT
10_1101-436634	320	7	variant	variant	NN
10_1101-436634	320	8	,	,	,
10_1101-436634	320	9	its	-PRON-	PRP$
10_1101-436634	320	10	mean_norm_score	mean_norm_score	NN
10_1101-436634	320	11	was	be	VBD
10_1101-436634	320	12	thus	thus	RB
10_1101-436634	320	13	equal	equal	JJ
10_1101-436634	320	14	to	to	IN
10_1101-436634	320	15	its	-PRON-	PRP$
10_1101-436634	320	16	norm_score	norm_score	NN
10_1101-436634	320	17	.	.	.
10_1101-436634	321	1	This	this	DT
10_1101-436634	321	2	value	value	NN
10_1101-436634	321	3	was	be	VBD
10_1101-436634	321	4	then	then	RB
10_1101-436634	321	5	compared	compare	VBN
10_1101-436634	321	6	to	to	IN
10_1101-436634	321	7	the	the	DT
10_1101-436634	321	8	distribution	distribution	NN
10_1101-436634	321	9	of	of	IN
10_1101-436634	321	10	samples	sample	NNS
10_1101-436634	321	11	which	which	WDT
10_1101-436634	321	12	did	do	VBD
10_1101-436634	321	13	not	not	RB
10_1101-436634	321	14	contain	contain	VB
10_1101-436634	321	15	the	the	DT
10_1101-436634	321	16	variant	variant	NN
10_1101-436634	321	17	to	to	TO
10_1101-436634	321	18	calculate	calculate	VB
10_1101-436634	321	19	a	a	DT
10_1101-436634	321	20	p	p	NN
10_1101-436634	321	21	-	-	HYPH
10_1101-436634	321	22	value	value	NN
10_1101-436634	321	23	as	as	IN
10_1101-436634	321	24	the	the	DT
10_1101-436634	321	25	percentage	percentage	NN
10_1101-436634	321	26	of	of	IN
10_1101-436634	321	27	the	the	DT
10_1101-436634	321	28	norm_scores	norm_scores	NNPS
10_1101-436634	321	29	from	from	IN
10_1101-436634	321	30	these	these	DT
10_1101-436634	321	31	samples	sample	NNS
10_1101-436634	321	32	which	which	WDT
10_1101-436634	321	33	are	be	VBP
10_1101-436634	321	34	at	at	IN
10_1101-436634	321	35	least	least	JJS
10_1101-436634	321	36	as	as	RB
10_1101-436634	321	37	high	high	JJ
10_1101-436634	321	38	as	as	IN
10_1101-436634	321	39	the	the	DT
10_1101-436634	321	40	mean_norm_score	mean_norm_score	NN
10_1101-436634	321	41	computed	compute	VBD
10_1101-436634	321	42	for	for	IN
10_1101-436634	321	43	the	the	DT
10_1101-436634	321	44	variant	variant	NN
10_1101-436634	321	45	-	-	HYPH
10_1101-436634	321	46	containing	contain	VBG
10_1101-436634	321	47	samples	sample	NNS
10_1101-436634	321	48	.	.	.
10_1101-436634	322	1	We	-PRON-	PRP
10_1101-436634	322	2	performed	perform	VBD
10_1101-436634	322	3	separate	separate	JJ
10_1101-436634	322	4	analyses	analysis	NNS
10_1101-436634	322	5	for	for	IN
10_1101-436634	322	6	events	event	NNS
10_1101-436634	322	7	involving	involve	VBG
10_1101-436634	322	8	canonical	canonical	JJ
10_1101-436634	322	9	junctions	junction	NNS
10_1101-436634	322	10	(	(	-LRB-
10_1101-436634	322	11	DA	DA	NNP
10_1101-436634	322	12	)	)	-RRB-
10_1101-436634	322	13	and	and	CC
10_1101-436634	322	14	those	those	DT
10_1101-436634	322	15	involving	involve	VBG
10_1101-436634	322	16	novel	novel	JJ
10_1101-436634	322	17	junctions	junction	NNS
10_1101-436634	322	18	which	which	WDT
10_1101-436634	322	19	used	use	VBD
10_1101-436634	322	20	at	at	RB
10_1101-436634	322	21	least	least	RBS
10_1101-436634	322	22	one	one	CD
10_1101-436634	322	23	known	know	VBN
10_1101-436634	322	24	splice	splice	NN
10_1101-436634	322	25	site	site	NN
10_1101-436634	322	26	(	(	-LRB-
10_1101-436634	322	27	D	D	NNP
10_1101-436634	322	28	/	/	SYM
10_1101-436634	322	29	A	A	NNP
10_1101-436634	322	30	/	/	SYM
10_1101-436634	322	31	NDA	NDA	NNP
10_1101-436634	322	32	)	)	-RRB-
10_1101-436634	322	33	,	,	,
10_1101-436634	322	34	based	base	VBN
10_1101-436634	322	35	on	on	IN
10_1101-436634	322	36	annotations	annotation	NNS
10_1101-436634	322	37	in	in	IN
10_1101-436634	322	38	the	the	DT
10_1101-436634	322	39	corresponding	corresponding	JJ
10_1101-436634	322	40	reference	reference	NN
10_1101-436634	322	41	GTF	gtf	NN
10_1101-436634	322	42	.	.	.
10_1101-436634	323	1	For	for	IN
10_1101-436634	323	2	this	this	DT
10_1101-436634	323	3	study	study	NN
10_1101-436634	323	4	,	,	,
10_1101-436634	323	5	we	-PRON-	PRP
10_1101-436634	323	6	filtered	filter	VBD
10_1101-436634	323	7	out	out	RP
10_1101-436634	323	8	any	any	DT
10_1101-436634	323	9	junctions	junction	NNS
10_1101-436634	323	10	which	which	WDT
10_1101-436634	323	11	did	do	VBD
10_1101-436634	323	12	not	not	RB
10_1101-436634	323	13	use	use	VB
10_1101-436634	323	14	at	at	RB
10_1101-436634	323	15	least	least	RBS
10_1101-436634	323	16	one	one	CD
10_1101-436634	323	17	known	know	VBN
10_1101-436634	323	18	splice	splice	NN
10_1101-436634	323	19	site	site	NN
10_1101-436634	323	20	(	(	-LRB-
10_1101-436634	323	21	N	n	NN
10_1101-436634	323	22	)	)	-RRB-
10_1101-436634	323	23	and	and	CC
10_1101-436634	323	24	junctions	junction	NNS
10_1101-436634	323	25	which	which	WDT
10_1101-436634	323	26	did	do	VBD
10_1101-436634	323	27	not	not	RB
10_1101-436634	323	28	have	have	VB
10_1101-436634	323	29	at	at	RB
10_1101-436634	323	30	least	least	RBS
10_1101-436634	323	31	5	5	CD
10_1101-436634	323	32	reads	read	NNS
10_1101-436634	323	33	of	of	IN
10_1101-436634	323	34	evidence	evidence	NN
10_1101-436634	323	35	across	across	IN
10_1101-436634	323	36	variant	variant	NN
10_1101-436634	323	37	-	-	HYPH
10_1101-436634	323	38	containing	contain	VBG
10_1101-436634	323	39	samples	sample	NNS
10_1101-436634	323	40	.	.	.
10_1101-436634	324	1	The	the	DT
10_1101-436634	324	2	Benjamini	Benjamini	NNP
10_1101-436634	324	3	-	-	HYPH
10_1101-436634	324	4	Hochberg	Hochberg	NNP
10_1101-436634	324	5	procedure	procedure	NN
10_1101-436634	324	6	was	be	VBD
10_1101-436634	324	7	then	then	RB
10_1101-436634	324	8	applied	apply	VBN
10_1101-436634	324	9	to	to	IN
10_1101-436634	324	10	the	the	DT
10_1101-436634	324	11	remaining	remain	VBG
10_1101-436634	324	12	events	event	NNS
10_1101-436634	324	13	.	.	.
10_1101-436634	325	1	Following	follow	VBG
10_1101-436634	325	2	correction	correction	NN
10_1101-436634	325	3	,	,	,
10_1101-436634	325	4	an	an	DT
10_1101-436634	325	5	event	event	NN
10_1101-436634	325	6	was	be	VBD
10_1101-436634	325	7	considered	consider	VBN
10_1101-436634	325	8	significant	significant	JJ
10_1101-436634	325	9	if	if	IN
10_1101-436634	325	10	its	-PRON-	PRP$
10_1101-436634	325	11	adjusted	adjusted	JJ
10_1101-436634	325	12	p	p	NN
10_1101-436634	325	13	-	-	HYPH
10_1101-436634	325	14	value	value	NN
10_1101-436634	325	15	was	be	VBD
10_1101-436634	325	16	≤	≤	NNP
10_1101-436634	325	17	0.05	0.05	CD
10_1101-436634	325	18	.	.	.
10_1101-436634	326	1	Annotation	annotation	NN
10_1101-436634	326	2	with	with	IN
10_1101-436634	326	3	GTEx	GTEx	NNP
10_1101-436634	326	4	junction	junction	NN
10_1101-436634	326	5	data	datum	NNS
10_1101-436634	326	6	and	and	CC
10_1101-436634	326	7	other	other	JJ
10_1101-436634	326	8	splice	splice	NN
10_1101-436634	326	9	prediction	prediction	NN
10_1101-436634	326	10	tools	tool	NNS
10_1101-436634	326	11	Events	event	NNS
10_1101-436634	326	12	identified	identify	VBN
10_1101-436634	326	13	by	by	IN
10_1101-436634	326	14	RegTools	regtool	NNS
10_1101-436634	326	15	as	as	IN
10_1101-436634	326	16	significant	significant	JJ
10_1101-436634	326	17	were	be	VBD
10_1101-436634	326	18	annotated	annotate	VBN
10_1101-436634	326	19	with	with	IN
10_1101-436634	326	20	information	information	NN
10_1101-436634	326	21	from	from	IN
10_1101-436634	326	22	GTEx	GTEx	NNS
10_1101-436634	326	23	,	,	,
10_1101-436634	326	24	VEP	VEP	NNP
10_1101-436634	326	25	,	,	,
10_1101-436634	326	26	SpliceAI	SpliceAI	NNP
10_1101-436634	326	27	,	,	,
10_1101-436634	326	28	MiSplice	MiSplice	NNP
10_1101-436634	326	29	,	,	,
10_1101-436634	326	30	and	and	CC
10_1101-436634	326	31	Veridical	veridical	JJ
10_1101-436634	326	32	.	.	.
10_1101-436634	327	1	GTEx	GTEx	NNS
10_1101-436634	327	2	junction	junction	NN
10_1101-436634	327	3	information	information	NN
10_1101-436634	327	4	was	be	VBD
10_1101-436634	327	5	obtained	obtain	VBN
10_1101-436634	327	6	from	from	IN
10_1101-436634	327	7	the	the	DT
10_1101-436634	327	8	GTEx	GTEx	NNP
10_1101-436634	327	9	Portal	Portal	NNP
10_1101-436634	327	10	.	.	.
10_1101-436634	328	1	Specifically	specifically	RB
10_1101-436634	328	2	,	,	,
10_1101-436634	328	3	the	the	DT
10_1101-436634	328	4	exon	exon	NN
10_1101-436634	328	5	-	-	HYPH
10_1101-436634	328	6	exon	exon	JJ
10_1101-436634	328	7	junction	junction	NN
10_1101-436634	328	8	read	read	VBD
10_1101-436634	328	9	counts	count	NNS
10_1101-436634	328	10	file	file	NN
10_1101-436634	328	11	from	from	IN
10_1101-436634	328	12	the	the	DT
10_1101-436634	328	13	v8	v8	NN
10_1101-436634	328	14	release	release	NN
10_1101-436634	328	15	was	be	VBD
10_1101-436634	328	16	used	use	VBN
10_1101-436634	328	17	for	for	IN
10_1101-436634	328	18	data	datum	NNS
10_1101-436634	328	19	aligned	align	VBN
10_1101-436634	328	20	to	to	IN
10_1101-436634	328	21	GRCh38	GRCh38	NNP
10_1101-436634	328	22	while	while	IN
10_1101-436634	328	23	the	the	DT
10_1101-436634	328	24	same	same	JJ
10_1101-436634	328	25	file	file	NN
10_1101-436634	328	26	from	from	IN
10_1101-436634	328	27	the	the	DT
10_1101-436634	328	28	v7	v7	NNP
10_1101-436634	328	29	release	release	NN
10_1101-436634	328	30	was	be	VBD
10_1101-436634	328	31	used	use	VBN
10_1101-436634	328	32	for	for	IN
10_1101-436634	328	33	the	the	DT
10_1101-436634	328	34	data	datum	NNS
10_1101-436634	328	35	aligned	align	VBN
10_1101-436634	328	36	to	to	IN
10_1101-436634	328	37	.CC	.CC	:
10_1101-436634	328	38	-	-	:
10_1101-436634	328	39	BY	by	IN
10_1101-436634	328	40	-	-	HYPH
10_1101-436634	328	41	NC	NC	NNP
10_1101-436634	328	42	-	-	HYPH
10_1101-436634	328	43	ND	ND	NNP
10_1101-436634	328	44	4.0	4.0	CD
10_1101-436634	328	45	International	international	JJ
10_1101-436634	328	46	licensea	licensea	NNS
10_1101-436634	328	47	certified	certify	VBN
10_1101-436634	328	48	by	by	IN
10_1101-436634	328	49	peer	peer	NN
10_1101-436634	328	50	review	review	NN
10_1101-436634	328	51	)	)	-RRB-
10_1101-436634	328	52	is	be	VBZ
10_1101-436634	328	53	the	the	DT
10_1101-436634	328	54	author	author	NN
10_1101-436634	328	55	/	/	SYM
10_1101-436634	328	56	funder	funder	NN
10_1101-436634	328	57	,	,	,
10_1101-436634	328	58	who	who	WP
10_1101-436634	328	59	has	have	VBZ
10_1101-436634	328	60	granted	grant	VBN
10_1101-436634	328	61	bioRxiv	biorxiv	IN
10_1101-436634	328	62	a	a	DT
10_1101-436634	328	63	license	license	NN
10_1101-436634	328	64	to	to	TO
10_1101-436634	328	65	display	display	VB
10_1101-436634	328	66	the	the	DT
10_1101-436634	328	67	preprint	preprint	NN
10_1101-436634	328	68	in	in	IN
10_1101-436634	328	69	perpetuity	perpetuity	NN
10_1101-436634	328	70	.	.	.
10_1101-436634	329	1	It	-PRON-	PRP
10_1101-436634	329	2	is	be	VBZ
10_1101-436634	329	3	made	make	VBN
10_1101-436634	329	4	available	available	JJ
10_1101-436634	329	5	under	under	IN
10_1101-436634	329	6	The	the	DT
10_1101-436634	329	7	copyright	copyright	NN
10_1101-436634	329	8	holder	holder	NN
10_1101-436634	329	9	for	for	IN
10_1101-436634	329	10	this	this	DT
10_1101-436634	329	11	preprint	preprint	NN
10_1101-436634	329	12	(	(	-LRB-
10_1101-436634	329	13	which	which	WDT
10_1101-436634	329	14	was	be	VBD
10_1101-436634	329	15	notthis	notthis	DT
10_1101-436634	329	16	version	version	NN
10_1101-436634	329	17	posted	post	VBN
10_1101-436634	329	18	January	January	NNP
10_1101-436634	329	19	5	5	CD
10_1101-436634	329	20	,	,	,
10_1101-436634	329	21	2021	2021	CD
10_1101-436634	329	22	.	.	.
10_1101-436634	329	23	;	;	:
10_1101-436634	329	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	329	25	:	:	:
10_1101-436634	329	26	bioRxiv	biorxiv	VB
10_1101-436634	329	27	preprint	preprint	NN
10_1101-436634	329	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	329	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	329	30	16	16	CD
10_1101-436634	329	31	GRCh37	GRCh37	NNS
10_1101-436634	329	32	.	.	.
10_1101-436634	330	1	Mappings	mapping	NNS
10_1101-436634	330	2	between	between	IN
10_1101-436634	330	3	tumor	tumor	NN
10_1101-436634	330	4	cohorts	cohort	NNS
10_1101-436634	330	5	and	and	CC
10_1101-436634	330	6	GTEx	GTEx	NNS
10_1101-436634	330	7	tissues	tissue	NNS
10_1101-436634	330	8	can	can	MD
10_1101-436634	330	9	be	be	VB
10_1101-436634	330	10	found	find	VBN
10_1101-436634	330	11	in	in	IN
10_1101-436634	330	12	Supplemental	Supplemental	NNP
10_1101-436634	330	13	File	File	NNP
10_1101-436634	330	14	7	7	CD
10_1101-436634	330	15	.	.	.
10_1101-436634	331	1	We	-PRON-	PRP
10_1101-436634	331	2	annotated	annotate	VBD
10_1101-436634	331	3	all	all	DT
10_1101-436634	331	4	starting	start	VBG
10_1101-436634	331	5	variants	variant	NNS
10_1101-436634	331	6	with	with	IN
10_1101-436634	331	7	VEP	VEP	NNP
10_1101-436634	331	8	in	in	IN
10_1101-436634	331	9	the	the	DT
10_1101-436634	331	10	“	"	``
10_1101-436634	331	11	per_gene	per_gene	NNP
10_1101-436634	331	12	”	"	''
10_1101-436634	331	13	and	and	CC
10_1101-436634	331	14	“	"	``
10_1101-436634	331	15	pick	pick	VB
10_1101-436634	331	16	”	"	''
10_1101-436634	331	17	modes	mode	NNS
10_1101-436634	331	18	.	.	.
10_1101-436634	332	1	The	the	DT
10_1101-436634	332	2	“	"	``
10_1101-436634	332	3	per_gene	per_gene	NNP
10_1101-436634	332	4	”	"	''
10_1101-436634	332	5	setting	set	VBG
10_1101-436634	332	6	outputs	output	NNS
10_1101-436634	332	7	only	only	RB
10_1101-436634	332	8	the	the	DT
10_1101-436634	332	9	most	most	RBS
10_1101-436634	332	10	severe	severe	JJ
10_1101-436634	332	11	consequence	consequence	NN
10_1101-436634	332	12	per	per	IN
10_1101-436634	332	13	gene	gene	NN
10_1101-436634	332	14	while	while	IN
10_1101-436634	332	15	the	the	DT
10_1101-436634	332	16	“	"	``
10_1101-436634	332	17	pick	pick	NN
10_1101-436634	332	18	”	"	''
10_1101-436634	332	19	setting	set	VBG
10_1101-436634	332	20	picks	pick	NNS
10_1101-436634	332	21	one	one	CD
10_1101-436634	332	22	line	line	NN
10_1101-436634	332	23	or	or	CC
10_1101-436634	332	24	block	block	NN
10_1101-436634	332	25	of	of	IN
10_1101-436634	332	26	consequence	consequence	NN
10_1101-436634	332	27	data	datum	NNS
10_1101-436634	332	28	per	per	IN
10_1101-436634	332	29	variant	variant	NN
10_1101-436634	332	30	.	.	.
10_1101-436634	333	1	We	-PRON-	PRP
10_1101-436634	333	2	considered	consider	VBD
10_1101-436634	333	3	any	any	DT
10_1101-436634	333	4	variant	variant	NN
10_1101-436634	333	5	with	with	IN
10_1101-436634	333	6	at	at	RB
10_1101-436634	333	7	least	least	RBS
10_1101-436634	333	8	one	one	CD
10_1101-436634	333	9	splicing	splicing	NN
10_1101-436634	333	10	-	-	HYPH
10_1101-436634	333	11	related	relate	VBN
10_1101-436634	333	12	annotation	annotation	NN
10_1101-436634	333	13	to	to	TO
10_1101-436634	333	14	be	be	VB
10_1101-436634	333	15	“	"	``
10_1101-436634	333	16	VEP	VEP	NNP
10_1101-436634	333	17	significant	significant	JJ
10_1101-436634	333	18	”	"	''
10_1101-436634	333	19	.	.	.
10_1101-436634	334	1	All	all	DT
10_1101-436634	334	2	variants	variant	NNS
10_1101-436634	334	3	were	be	VBD
10_1101-436634	334	4	also	also	RB
10_1101-436634	334	5	processed	process	VBN
10_1101-436634	334	6	with	with	IN
10_1101-436634	334	7	SpliceAI	SpliceAI	NNP
10_1101-436634	334	8	using	use	VBG
10_1101-436634	334	9	the	the	DT
10_1101-436634	334	10	default	default	NN
10_1101-436634	334	11	options	option	NNS
10_1101-436634	334	12	.	.	.
10_1101-436634	335	1	A	a	DT
10_1101-436634	335	2	variant	variant	NN
10_1101-436634	335	3	was	be	VBD
10_1101-436634	335	4	considered	consider	VBN
10_1101-436634	335	5	to	to	TO
10_1101-436634	335	6	be	be	VB
10_1101-436634	335	7	“	"	``
10_1101-436634	335	8	SpliceAI	spliceai	JJ
10_1101-436634	335	9	significant	significant	JJ
10_1101-436634	335	10	”	"	''
10_1101-436634	335	11	if	if	IN
10_1101-436634	335	12	it	-PRON-	PRP
10_1101-436634	335	13	had	have	VBD
10_1101-436634	335	14	at	at	RB
10_1101-436634	335	15	least	least	RBS
10_1101-436634	335	16	one	one	CD
10_1101-436634	335	17	score	score	NN
10_1101-436634	335	18	greater	great	JJR
10_1101-436634	335	19	than	than	IN
10_1101-436634	335	20	0.2	0.2	CD
10_1101-436634	335	21	,	,	,
10_1101-436634	335	22	the	the	DT
10_1101-436634	335	23	developers	developer	NNS
10_1101-436634	335	24	’	’	POS
10_1101-436634	335	25	value	value	NN
10_1101-436634	335	26	for	for	IN
10_1101-436634	335	27	high	high	JJ
10_1101-436634	335	28	recall	recall	NN
10_1101-436634	335	29	of	of	IN
10_1101-436634	335	30	their	-PRON-	PRP$
10_1101-436634	335	31	model	model	NN
10_1101-436634	335	32	.	.	.
10_1101-436634	336	1	Variants	variant	NNS
10_1101-436634	336	2	identified	identify	VBN
10_1101-436634	336	3	by	by	IN
10_1101-436634	336	4	MiSplice20	misplice20	CD
10_1101-436634	336	5	were	be	VBD
10_1101-436634	336	6	obtained	obtain	VBN
10_1101-436634	336	7	from	from	IN
10_1101-436634	336	8	the	the	DT
10_1101-436634	336	9	paper	paper	NN
10_1101-436634	336	10	supplemental	supplemental	JJ
10_1101-436634	336	11	tables	table	NNS
10_1101-436634	336	12	and	and	CC
10_1101-436634	336	13	were	be	VBD
10_1101-436634	336	14	lifted	lift	VBN
10_1101-436634	336	15	over	over	RP
10_1101-436634	336	16	to	to	IN
10_1101-436634	336	17	GRCh38	GRCh38	NNP
10_1101-436634	336	18	.	.	.
10_1101-436634	337	1	Variants	variant	NNS
10_1101-436634	337	2	identified	identify	VBN
10_1101-436634	337	3	by	by	IN
10_1101-436634	337	4	SAVNet23	SAVNet23	NNP
10_1101-436634	337	5	were	be	VBD
10_1101-436634	337	6	obtained	obtain	VBN
10_1101-436634	337	7	from	from	IN
10_1101-436634	337	8	the	the	DT
10_1101-436634	337	9	paper	paper	NN
10_1101-436634	337	10	supplemental	supplemental	JJ
10_1101-436634	337	11	tables	table	NNS
10_1101-436634	337	12	and	and	CC
10_1101-436634	337	13	were	be	VBD
10_1101-436634	337	14	lifted	lift	VBN
10_1101-436634	337	15	over	over	RP
10_1101-436634	337	16	to	to	IN
10_1101-436634	337	17	GRCh38	GRCh38	NNP
10_1101-436634	337	18	.	.	.
10_1101-436634	338	1	Variants	variant	NNS
10_1101-436634	338	2	identified	identify	VBN
10_1101-436634	338	3	by	by	IN
10_1101-436634	338	4	Veridical21,22	Veridical21,22	NNP
10_1101-436634	338	5	were	be	VBD
10_1101-436634	338	6	obtained	obtain	VBN
10_1101-436634	338	7	via	via	IN
10_1101-436634	338	8	download	download	NN
10_1101-436634	338	9	from	from	IN
10_1101-436634	338	10	the	the	DT
10_1101-436634	338	11	link	link	NN
10_1101-436634	338	12	reference	reference	NN
10_1101-436634	338	13	within	within	IN
10_1101-436634	338	14	the	the	DT
10_1101-436634	338	15	manuscript	manuscript	NN
10_1101-436634	338	16	and	and	CC
10_1101-436634	338	17	lifted	lift	VBD
10_1101-436634	338	18	over	over	RP
10_1101-436634	338	19	to	to	IN
10_1101-436634	338	20	GRCh38	GRCh38	NNP
10_1101-436634	338	21	.	.	.
10_1101-436634	339	1	Visual	visual	JJ
10_1101-436634	339	2	exploration	exploration	NN
10_1101-436634	339	3	of	of	IN
10_1101-436634	339	4	statistically	statistically	RB
10_1101-436634	339	5	significant	significant	JJ
10_1101-436634	339	6	candidate	candidate	NN
10_1101-436634	339	7	events	event	NNS
10_1101-436634	339	8	IGV	IGV	NNP
10_1101-436634	339	9	sessions	session	NNS
10_1101-436634	339	10	were	be	VBD
10_1101-436634	339	11	created	create	VBN
10_1101-436634	339	12	for	for	IN
10_1101-436634	339	13	each	each	DT
10_1101-436634	339	14	event	event	NN
10_1101-436634	339	15	identified	identify	VBN
10_1101-436634	339	16	by	by	IN
10_1101-436634	339	17	RegTools	regtool	NNS
10_1101-436634	339	18	that	that	WDT
10_1101-436634	339	19	was	be	VBD
10_1101-436634	339	20	statistically	statistically	RB
10_1101-436634	339	21	significant	significant	JJ
10_1101-436634	339	22	.	.	.
10_1101-436634	340	1	Each	each	DT
10_1101-436634	340	2	IGV	igv	NN
10_1101-436634	340	3	session	session	NN
10_1101-436634	340	4	file	file	NN
10_1101-436634	340	5	contained	contain	VBD
10_1101-436634	340	6	a	a	DT
10_1101-436634	340	7	bed	bed	NN
10_1101-436634	340	8	file	file	NN
10_1101-436634	340	9	with	with	IN
10_1101-436634	340	10	the	the	DT
10_1101-436634	340	11	junction	junction	NN
10_1101-436634	340	12	,	,	,
10_1101-436634	340	13	a	a	DT
10_1101-436634	340	14	vcf	vcf	NN
10_1101-436634	340	15	file	file	NN
10_1101-436634	340	16	with	with	IN
10_1101-436634	340	17	the	the	DT
10_1101-436634	340	18	variant	variant	NN
10_1101-436634	340	19	,	,	,
10_1101-436634	340	20	and	and	CC
10_1101-436634	340	21	an	an	DT
10_1101-436634	340	22	alignment	alignment	NN
10_1101-436634	340	23	file	file	NN
10_1101-436634	340	24	for	for	IN
10_1101-436634	340	25	each	each	DT
10_1101-436634	340	26	sample	sample	NN
10_1101-436634	340	27	that	that	WDT
10_1101-436634	340	28	contained	contain	VBD
10_1101-436634	340	29	the	the	DT
10_1101-436634	340	30	variant	variant	NN
10_1101-436634	340	31	.	.	.
10_1101-436634	341	1	Additional	additional	JJ
10_1101-436634	341	2	information	information	NN
10_1101-436634	341	3	,	,	,
10_1101-436634	341	4	such	such	JJ
10_1101-436634	341	5	as	as	IN
10_1101-436634	341	6	the	the	DT
10_1101-436634	341	7	splice	splice	NN
10_1101-436634	341	8	sites	site	NNS
10_1101-436634	341	9	predicted	predict	VBN
10_1101-436634	341	10	by	by	IN
10_1101-436634	341	11	SpliceAI	spliceai	CD
10_1101-436634	341	12	,	,	,
10_1101-436634	341	13	were	be	VBD
10_1101-436634	341	14	also	also	RB
10_1101-436634	341	15	added	add	VBN
10_1101-436634	341	16	to	to	IN
10_1101-436634	341	17	these	these	DT
10_1101-436634	341	18	session	session	NN
10_1101-436634	341	19	files	file	NNS
10_1101-436634	341	20	to	to	TO
10_1101-436634	341	21	enhance	enhance	VB
10_1101-436634	341	22	the	the	DT
10_1101-436634	341	23	exploration	exploration	NN
10_1101-436634	341	24	of	of	IN
10_1101-436634	341	25	these	these	DT
10_1101-436634	341	26	events	event	NNS
10_1101-436634	341	27	.	.	.
10_1101-436634	342	1	Events	event	NNS
10_1101-436634	342	2	of	of	IN
10_1101-436634	342	3	interest	interest	NN
10_1101-436634	342	4	were	be	VBD
10_1101-436634	342	5	manually	manually	RB
10_1101-436634	342	6	reviewed	review	VBN
10_1101-436634	342	7	in	in	IN
10_1101-436634	342	8	IGV	IGV	NNP
10_1101-436634	342	9	to	to	TO
10_1101-436634	342	10	assess	assess	VB
10_1101-436634	342	11	whether	whether	IN
10_1101-436634	342	12	the	the	DT
10_1101-436634	342	13	association	association	NN
10_1101-436634	342	14	between	between	IN
10_1101-436634	342	15	the	the	DT
10_1101-436634	342	16	variant	variant	JJ
10_1101-436634	342	17	and	and	CC
10_1101-436634	342	18	junction	junction	NN
10_1101-436634	342	19	made	make	VBD
10_1101-436634	342	20	sense	sense	NN
10_1101-436634	342	21	in	in	IN
10_1101-436634	342	22	a	a	DT
10_1101-436634	342	23	biological	biological	JJ
10_1101-436634	342	24	context	context	NN
10_1101-436634	342	25	(	(	-LRB-
10_1101-436634	342	26	e.g.	e.g.	RB
10_1101-436634	343	1	affected	affect	VBD
10_1101-436634	343	2	a	a	DT
10_1101-436634	343	3	known	know	VBN
10_1101-436634	343	4	splice	splice	NN
10_1101-436634	343	5	site	site	NN
10_1101-436634	343	6	,	,	,
10_1101-436634	343	7	altered	alter	VBD
10_1101-436634	343	8	a	a	DT
10_1101-436634	343	9	genomic	genomic	JJ
10_1101-436634	343	10	sequence	sequence	NN
10_1101-436634	343	11	to	to	TO
10_1101-436634	343	12	look	look	VB
10_1101-436634	343	13	more	more	JJR
10_1101-436634	343	14	like	like	IN
10_1101-436634	343	15	a	a	DT
10_1101-436634	343	16	canonical	canonical	JJ
10_1101-436634	343	17	splice	splice	NN
10_1101-436634	343	18	site	site	NN
10_1101-436634	343	19	,	,	,
10_1101-436634	343	20	or	or	CC
10_1101-436634	343	21	the	the	DT
10_1101-436634	343	22	novel	novel	JJ
10_1101-436634	343	23	junction	junction	NN
10_1101-436634	343	24	disrupted	disrupt	VBD
10_1101-436634	343	25	active	active	JJ
10_1101-436634	343	26	or	or	CC
10_1101-436634	343	27	regulatory	regulatory	JJ
10_1101-436634	343	28	domains	domain	NNS
10_1101-436634	343	29	of	of	IN
10_1101-436634	343	30	the	the	DT
10_1101-436634	343	31	protein	protein	NN
10_1101-436634	343	32	product	product	NN
10_1101-436634	343	33	)	)	-RRB-
10_1101-436634	343	34	.	.	.
10_1101-436634	344	1	An	an	DT
10_1101-436634	344	2	extensive	extensive	JJ
10_1101-436634	344	3	review	review	NN
10_1101-436634	344	4	of	of	IN
10_1101-436634	344	5	literature	literature	NN
10_1101-436634	344	6	and	and	CC
10_1101-436634	344	7	visualizations	visualization	NNS
10_1101-436634	344	8	of	of	IN
10_1101-436634	344	9	junction	junction	NN
10_1101-436634	344	10	usage	usage	NN
10_1101-436634	344	11	in	in	IN
10_1101-436634	344	12	the	the	DT
10_1101-436634	344	13	presence	presence	NN
10_1101-436634	344	14	and	and	CC
10_1101-436634	344	15	absence	absence	NN
10_1101-436634	344	16	of	of	IN
10_1101-436634	344	17	the	the	DT
10_1101-436634	344	18	variant	variant	NN
10_1101-436634	344	19	were	be	VBD
10_1101-436634	344	20	also	also	RB
10_1101-436634	344	21	used	use	VBN
10_1101-436634	344	22	to	to	TO
10_1101-436634	344	23	identify	identify	VB
10_1101-436634	344	24	novel	novel	NN
10_1101-436634	344	25	,	,	,
10_1101-436634	344	26	biologically	biologically	RB
10_1101-436634	344	27	relevant	relevant	JJ
10_1101-436634	344	28	events	event	NNS
10_1101-436634	344	29	.	.	.
10_1101-436634	345	1	Identification	identification	NN
10_1101-436634	345	2	of	of	IN
10_1101-436634	345	3	genes	gene	NNS
10_1101-436634	345	4	with	with	IN
10_1101-436634	345	5	recurrent	recurrent	JJ
10_1101-436634	345	6	splice	splice	NN
10_1101-436634	345	7	altering	alter	VBG
10_1101-436634	345	8	variants	variant	NNS
10_1101-436634	345	9	For	for	IN
10_1101-436634	345	10	each	each	DT
10_1101-436634	345	11	cohort	cohort	NN
10_1101-436634	345	12	,	,	,
10_1101-436634	345	13	we	-PRON-	PRP
10_1101-436634	345	14	calculated	calculate	VBD
10_1101-436634	345	15	a	a	DT
10_1101-436634	345	16	p	p	NN
10_1101-436634	345	17	-	-	HYPH
10_1101-436634	345	18	value	value	NN
10_1101-436634	345	19	to	to	TO
10_1101-436634	345	20	assess	assess	VB
10_1101-436634	345	21	whether	whether	IN
10_1101-436634	345	22	the	the	DT
10_1101-436634	345	23	splicing	splicing	NN
10_1101-436634	345	24	profile	profile	NN
10_1101-436634	345	25	from	from	IN
10_1101-436634	345	26	a	a	DT
10_1101-436634	345	27	particular	particular	JJ
10_1101-436634	345	28	gene	gene	NN
10_1101-436634	345	29	was	be	VBD
10_1101-436634	345	30	significantly	significantly	RB
10_1101-436634	345	31	more	more	RBR
10_1101-436634	345	32	likely	likely	JJ
10_1101-436634	345	33	to	to	TO
10_1101-436634	345	34	be	be	VB
10_1101-436634	345	35	altered	alter	VBN
10_1101-436634	345	36	by	by	IN
10_1101-436634	345	37	somatic	somatic	JJ
10_1101-436634	345	38	variants	variant	NNS
10_1101-436634	345	39	.	.	.
10_1101-436634	346	1	Specifically	specifically	RB
10_1101-436634	346	2	,	,	,
10_1101-436634	346	3	we	-PRON-	PRP
10_1101-436634	346	4	performed	perform	VBD
10_1101-436634	346	5	a	a	DT
10_1101-436634	346	6	1-tailed	1-tailed	CD
10_1101-436634	346	7	binomial	binomial	JJ
10_1101-436634	346	8	test	test	NN
10_1101-436634	346	9	,	,	,
10_1101-436634	346	10	considering	consider	VBG
10_1101-436634	346	11	the	the	DT
10_1101-436634	346	12	number	number	NN
10_1101-436634	346	13	of	of	IN
10_1101-436634	346	14	samples	sample	NNS
10_1101-436634	346	15	in	in	IN
10_1101-436634	346	16	a	a	DT
10_1101-436634	346	17	cohort	cohort	NN
10_1101-436634	346	18	as	as	IN
10_1101-436634	346	19	the	the	DT
10_1101-436634	346	20	number	number	NN
10_1101-436634	346	21	of	of	IN
10_1101-436634	346	22	attempts	attempt	NNS
10_1101-436634	346	23	.	.	.
10_1101-436634	347	1	Success	success	NN
10_1101-436634	347	2	was	be	VBD
10_1101-436634	347	3	defined	define	VBN
10_1101-436634	347	4	by	by	IN
10_1101-436634	347	5	whether	whether	IN
10_1101-436634	347	6	the	the	DT
10_1101-436634	347	7	sample	sample	NN
10_1101-436634	347	8	had	have	VBD
10_1101-436634	347	9	evidence	evidence	NN
10_1101-436634	347	10	of	of	IN
10_1101-436634	347	11	at	at	RB
10_1101-436634	347	12	least	least	RBS
10_1101-436634	347	13	one	one	CD
10_1101-436634	347	14	splice	splice	NN
10_1101-436634	347	15	-	-	HYPH
10_1101-436634	347	16	altering	alter	VBG
10_1101-436634	347	17	variant	variant	NN
10_1101-436634	347	18	in	in	IN
10_1101-436634	347	19	that	that	DT
10_1101-436634	347	20	gene	gene	NN
10_1101-436634	347	21	.	.	.
10_1101-436634	348	1	The	the	DT
10_1101-436634	348	2	null	null	JJ
10_1101-436634	348	3	probability	probability	NN
10_1101-436634	348	4	of	of	IN
10_1101-436634	348	5	success	success	NN
10_1101-436634	348	6	,	,	,
10_1101-436634	348	7	pnull	pnull	JJ
10_1101-436634	348	8	was	be	VBD
10_1101-436634	348	9	calculated	calculate	VBN
10_1101-436634	348	10	as	as	IN
10_1101-436634	348	11	where	where	WRB
10_1101-436634	348	12	s	s	POS
10_1101-436634	348	13	is	be	VBZ
10_1101-436634	348	14	the	the	DT
10_1101-436634	348	15	total	total	JJ
10_1101-436634	348	16	number	number	NN
10_1101-436634	348	17	of	of	IN
10_1101-436634	348	18	base	base	NN
10_1101-436634	348	19	positions	position	NNS
10_1101-436634	348	20	residing	reside	VBG
10_1101-436634	348	21	in	in	IN
10_1101-436634	348	22	any	any	DT
10_1101-436634	348	23	of	of	IN
10_1101-436634	348	24	the	the	DT
10_1101-436634	348	25	gene	gene	NN
10_1101-436634	348	26	’s	’s	POS
10_1101-436634	348	27	splice	splice	NN
10_1101-436634	348	28	variant	variant	JJ
10_1101-436634	348	29	windows	window	NNS
10_1101-436634	348	30	,	,	,
10_1101-436634	348	31	V	V	NNP
10_1101-436634	348	32	is	be	VBZ
10_1101-436634	348	33	the	the	DT
10_1101-436634	348	34	event	event	NN
10_1101-436634	348	35	that	that	WDT
10_1101-436634	348	36	a	a	DT
10_1101-436634	348	37	somatic	somatic	JJ
10_1101-436634	348	38	variant	variant	NN
10_1101-436634	348	39	occurred	occur	VBD
10_1101-436634	348	40	at	at	IN
10_1101-436634	348	41	such	such	PDT
10_1101-436634	348	42	a	a	DT
10_1101-436634	348	43	base	base	NN
10_1101-436634	348	44	position	position	NN
10_1101-436634	348	45	,	,	,
10_1101-436634	348	46	and	and	CC
10_1101-436634	348	47	A	a	DT
10_1101-436634	348	48	is	be	VBZ
10_1101-436634	348	49	the	the	DT
10_1101-436634	348	50	event	event	NN
10_1101-436634	348	51	that	that	IN
10_1101-436634	348	52	this	this	DT
10_1101-436634	348	53	variant	variant	NN
10_1101-436634	348	54	was	be	VBD
10_1101-436634	348	55	deemed	deem	VBN
10_1101-436634	348	56	to	to	TO
10_1101-436634	348	57	be	be	VB
10_1101-436634	348	58	significantly	significantly	RB
10_1101-436634	348	59	associated	associate	VBN
10_1101-436634	348	60	with	with	IN
10_1101-436634	348	61	at	at	RB
10_1101-436634	348	62	least	least	RBS
10_1101-436634	348	63	one	one	CD
10_1101-436634	348	64	junction	junction	NN
10_1101-436634	348	65	in	in	IN
10_1101-436634	348	66	our	-PRON-	PRP$
10_1101-436634	348	67	analysis	analysis	NN
10_1101-436634	348	68	.	.	.
10_1101-436634	349	1	The	the	DT
10_1101-436634	349	2	joint	joint	JJ
10_1101-436634	349	3	probability	probability	NN
10_1101-436634	349	4	that	that	IN
10_1101-436634	349	5	both	both	CC
10_1101-436634	349	6	V	V	NNP
10_1101-436634	349	7	and	and	CC
10_1101-436634	349	8	A	a	DT
10_1101-436634	349	9	occurred	occur	VBN
10_1101-436634	349	10	was	be	VBD
10_1101-436634	349	11	estimated	estimate	VBN
10_1101-436634	349	12	by	by	IN
10_1101-436634	349	13	dividing	divide	VBG
10_1101-436634	349	14	the	the	DT
10_1101-436634	349	15	total	total	NN
10_1101-436634	349	16	of	of	IN
10_1101-436634	349	17	events	event	NNS
10_1101-436634	349	18	across	across	IN
10_1101-436634	349	19	all	all	DT
10_1101-436634	349	20	samples	sample	NNS
10_1101-436634	349	21	in	in	IN
10_1101-436634	349	22	which	which	WDT
10_1101-436634	349	23	each	each	DT
10_1101-436634	349	24	junction	junction	NN
10_1101-436634	349	25	was	be	VBD
10_1101-436634	349	26	detected	detect	VBN
10_1101-436634	349	27	by	by	IN
10_1101-436634	349	28	s.	s.	NN
10_1101-436634	349	29	The	the	DT
10_1101-436634	349	30	value	value	NN
10_1101-436634	349	31	of	of	IN
10_1101-436634	349	32	s	s	POS
10_1101-436634	349	33	was	be	VBD
10_1101-436634	349	34	computed	compute	VBN
10_1101-436634	349	35	based	base	VBN
10_1101-436634	349	36	on	on	IN
10_1101-436634	349	37	the	the	DT
10_1101-436634	349	38	exon	exon	NN
10_1101-436634	349	39	and	and	CC
10_1101-436634	349	40	transcript	transcript	JJ
10_1101-436634	349	41	definitions	definition	NNS
10_1101-436634	349	42	in	in	IN
10_1101-436634	349	43	the	the	DT
10_1101-436634	349	44	reference	reference	NN
10_1101-436634	349	45	GTF	gtf	NN
10_1101-436634	349	46	used	use	VBN
10_1101-436634	349	47	for	for	IN
10_1101-436634	349	48	performing	perform	VBG
10_1101-436634	349	49	RegTools	RegTools	NNP
10_1101-436634	349	50	analyses	analysis	NNS
10_1101-436634	349	51	on	on	IN
10_1101-436634	349	52	a	a	DT
10_1101-436634	349	53	given	give	VBN
10_1101-436634	349	54	cohort	cohort	NN
10_1101-436634	349	55	.	.	.
10_1101-436634	350	1	.CC	.CC	NFP
10_1101-436634	350	2	-	-	:
10_1101-436634	350	3	BY	by	IN
10_1101-436634	350	4	-	-	HYPH
10_1101-436634	350	5	NC	NC	NNP
10_1101-436634	350	6	-	-	HYPH
10_1101-436634	350	7	ND	ND	NNP
10_1101-436634	350	8	4.0	4.0	CD
10_1101-436634	350	9	International	international	JJ
10_1101-436634	350	10	licensea	licensea	NNS
10_1101-436634	350	11	certified	certify	VBN
10_1101-436634	350	12	by	by	IN
10_1101-436634	350	13	peer	peer	NN
10_1101-436634	350	14	review	review	NN
10_1101-436634	350	15	)	)	-RRB-
10_1101-436634	350	16	is	be	VBZ
10_1101-436634	350	17	the	the	DT
10_1101-436634	350	18	author	author	NN
10_1101-436634	350	19	/	/	SYM
10_1101-436634	350	20	funder	funder	NN
10_1101-436634	350	21	,	,	,
10_1101-436634	350	22	who	who	WP
10_1101-436634	350	23	has	have	VBZ
10_1101-436634	350	24	granted	grant	VBN
10_1101-436634	350	25	bioRxiv	biorxiv	IN
10_1101-436634	350	26	a	a	DT
10_1101-436634	350	27	license	license	NN
10_1101-436634	350	28	to	to	TO
10_1101-436634	350	29	display	display	VB
10_1101-436634	350	30	the	the	DT
10_1101-436634	350	31	preprint	preprint	NN
10_1101-436634	350	32	in	in	IN
10_1101-436634	350	33	perpetuity	perpetuity	NN
10_1101-436634	350	34	.	.	.
10_1101-436634	351	1	It	-PRON-	PRP
10_1101-436634	351	2	is	be	VBZ
10_1101-436634	351	3	made	make	VBN
10_1101-436634	351	4	available	available	JJ
10_1101-436634	351	5	under	under	IN
10_1101-436634	351	6	The	the	DT
10_1101-436634	351	7	copyright	copyright	NN
10_1101-436634	351	8	holder	holder	NN
10_1101-436634	351	9	for	for	IN
10_1101-436634	351	10	this	this	DT
10_1101-436634	351	11	preprint	preprint	NN
10_1101-436634	351	12	(	(	-LRB-
10_1101-436634	351	13	which	which	WDT
10_1101-436634	351	14	was	be	VBD
10_1101-436634	351	15	notthis	notthis	DT
10_1101-436634	351	16	version	version	NN
10_1101-436634	351	17	posted	post	VBN
10_1101-436634	351	18	January	January	NNP
10_1101-436634	351	19	5	5	CD
10_1101-436634	351	20	,	,	,
10_1101-436634	351	21	2021	2021	CD
10_1101-436634	351	22	.	.	.
10_1101-436634	351	23	;	;	:
10_1101-436634	351	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	351	25	:	:	:
10_1101-436634	351	26	bioRxiv	biorxiv	VB
10_1101-436634	351	27	preprint	preprint	NN
10_1101-436634	351	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	351	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	351	30	17	17	CD
10_1101-436634	351	31	We	-PRON-	PRP
10_1101-436634	351	32	also	also	RB
10_1101-436634	351	33	calculated	calculate	VBD
10_1101-436634	351	34	overall	overall	JJ
10_1101-436634	351	35	metrics	metric	NNS
10_1101-436634	351	36	,	,	,
10_1101-436634	351	37	in	in	IN
10_1101-436634	351	38	order	order	NN
10_1101-436634	351	39	to	to	TO
10_1101-436634	351	40	rank	rank	VB
10_1101-436634	351	41	genes	gene	NNS
10_1101-436634	351	42	.	.	.
10_1101-436634	352	1	For	for	IN
10_1101-436634	352	2	each	each	DT
10_1101-436634	352	3	set	set	NN
10_1101-436634	352	4	of	of	IN
10_1101-436634	352	5	cohorts	cohort	NNS
10_1101-436634	352	6	(	(	-LRB-
10_1101-436634	352	7	e.g.	e.g.	RB
10_1101-436634	353	1	TCGA-	TCGA-	NNP
10_1101-436634	353	2	only	only	RB
10_1101-436634	353	3	,	,	,
10_1101-436634	353	4	MGI	MGI	NNP
10_1101-436634	353	5	-	-	HYPH
10_1101-436634	353	6	only	only	RB
10_1101-436634	353	7	,	,	,
10_1101-436634	353	8	combined	combine	VBN
10_1101-436634	353	9	)	)	-RRB-
10_1101-436634	353	10	,	,	,
10_1101-436634	353	11	an	an	DT
10_1101-436634	353	12	overall	overall	JJ
10_1101-436634	353	13	p	p	NN
10_1101-436634	353	14	-	-	HYPH
10_1101-436634	353	15	value	value	NN
10_1101-436634	353	16	was	be	VBD
10_1101-436634	353	17	computed	compute	VBN
10_1101-436634	353	18	for	for	IN
10_1101-436634	353	19	each	each	DT
10_1101-436634	353	20	gene	gene	NN
10_1101-436634	353	21	according	accord	VBG
10_1101-436634	353	22	to	to	IN
10_1101-436634	353	23	the	the	DT
10_1101-436634	353	24	above	above	JJ
10_1101-436634	353	25	formula	formula	NN
10_1101-436634	353	26	,	,	,
10_1101-436634	353	27	pooling	pool	VBG
10_1101-436634	353	28	all	all	DT
10_1101-436634	353	29	of	of	IN
10_1101-436634	353	30	the	the	DT
10_1101-436634	353	31	samples	sample	NNS
10_1101-436634	353	32	across	across	IN
10_1101-436634	353	33	the	the	DT
10_1101-436634	353	34	included	include	VBN
10_1101-436634	353	35	cohorts	cohort	NNS
10_1101-436634	353	36	,	,	,
10_1101-436634	353	37	and	and	CC
10_1101-436634	353	38	the	the	DT
10_1101-436634	353	39	fraction	fraction	NN
10_1101-436634	353	40	of	of	IN
10_1101-436634	353	41	samples	sample	NNS
10_1101-436634	353	42	was	be	VBD
10_1101-436634	353	43	simply	simply	RB
10_1101-436634	353	44	calculated	calculate	VBN
10_1101-436634	353	45	by	by	IN
10_1101-436634	353	46	dividing	divide	VBG
10_1101-436634	353	47	the	the	DT
10_1101-436634	353	48	number	number	NN
10_1101-436634	353	49	of	of	IN
10_1101-436634	353	50	samples	sample	NNS
10_1101-436634	353	51	in	in	IN
10_1101-436634	353	52	which	which	WDT
10_1101-436634	353	53	an	an	DT
10_1101-436634	353	54	event	event	NN
10_1101-436634	353	55	occurred	occur	VBD
10_1101-436634	353	56	within	within	IN
10_1101-436634	353	57	the	the	DT
10_1101-436634	353	58	given	give	VBN
10_1101-436634	353	59	gene	gene	NN
10_1101-436634	353	60	by	by	IN
10_1101-436634	353	61	the	the	DT
10_1101-436634	353	62	total	total	JJ
10_1101-436634	353	63	number	number	NN
10_1101-436634	353	64	of	of	IN
10_1101-436634	353	65	samples	sample	NNS
10_1101-436634	353	66	,	,	,
10_1101-436634	353	67	pooled	pool	VBN
10_1101-436634	353	68	across	across	IN
10_1101-436634	353	69	the	the	DT
10_1101-436634	353	70	included	included	JJ
10_1101-436634	353	71	cohorts	cohort	NNS
10_1101-436634	353	72	.	.	.
10_1101-436634	354	1	The	the	DT
10_1101-436634	354	2	reference	reference	NN
10_1101-436634	354	3	GTF	gtf	NN
10_1101-436634	354	4	used	use	VBN
10_1101-436634	354	5	for	for	IN
10_1101-436634	354	6	analyzing	analyze	VBG
10_1101-436634	354	7	the	the	DT
10_1101-436634	354	8	TCGA	TCGA	NNP
10_1101-436634	354	9	samples	sample	NNS
10_1101-436634	354	10	(	(	-LRB-
10_1101-436634	354	11	i.e.	i.e.	FW
10_1101-436634	355	1	gencode.v29.annotation.gtf	gencode.v29.annotation.gtf	NNP
10_1101-436634	355	2	)	)	-RRB-
10_1101-436634	355	3	was	be	VBD
10_1101-436634	355	4	used	use	VBN
10_1101-436634	355	5	for	for	IN
10_1101-436634	355	6	all	all	DT
10_1101-436634	355	7	sets	set	NNS
10_1101-436634	355	8	of	of	IN
10_1101-436634	355	9	cohorts	cohort	NNS
10_1101-436634	355	10	.	.	.
10_1101-436634	356	1	Code	code	NN
10_1101-436634	356	2	availability	availability	NN
10_1101-436634	356	3	RegTools	RegTools	NNP
10_1101-436634	356	4	is	be	VBZ
10_1101-436634	356	5	open	open	JJ
10_1101-436634	356	6	source	source	NN
10_1101-436634	356	7	(	(	-LRB-
10_1101-436634	356	8	MIT	MIT	NNP
10_1101-436634	356	9	license	license	NN
10_1101-436634	356	10	)	)	-RRB-
10_1101-436634	356	11	and	and	CC
10_1101-436634	356	12	available	available	JJ
10_1101-436634	356	13	at	at	IN
10_1101-436634	356	14	https://github.com/griffithlab/regtools/.	https://github.com/griffithlab/regtools/.	NNP
10_1101-436634	357	1	All	all	DT
10_1101-436634	357	2	scripts	script	NNS
10_1101-436634	357	3	used	use	VBN
10_1101-436634	357	4	in	in	IN
10_1101-436634	357	5	the	the	DT
10_1101-436634	357	6	analyses	analysis	NNS
10_1101-436634	357	7	presented	present	VBN
10_1101-436634	357	8	here	here	RB
10_1101-436634	357	9	are	be	VBP
10_1101-436634	357	10	also	also	RB
10_1101-436634	357	11	provided	provide	VBN
10_1101-436634	357	12	.	.	.
10_1101-436634	358	1	For	for	IN
10_1101-436634	358	2	ease	ease	NN
10_1101-436634	358	3	of	of	IN
10_1101-436634	358	4	use	use	NN
10_1101-436634	358	5	,	,	,
10_1101-436634	358	6	a	a	DT
10_1101-436634	358	7	Docker	Docker	NNP
10_1101-436634	358	8	container	container	NN
10_1101-436634	358	9	has	have	VBZ
10_1101-436634	358	10	been	be	VBN
10_1101-436634	358	11	created	create	VBN
10_1101-436634	358	12	with	with	IN
10_1101-436634	358	13	RegTools	RegTools	NNP
10_1101-436634	358	14	,	,	,
10_1101-436634	358	15	R	r	NN
10_1101-436634	358	16	,	,	,
10_1101-436634	358	17	and	and	CC
10_1101-436634	358	18	Python	Python	NNP
10_1101-436634	358	19	3	3	CD
10_1101-436634	358	20	installed	instal	VBN
10_1101-436634	358	21	(	(	-LRB-
10_1101-436634	358	22	https://hub.docker.com/r/griffithlab/regtools/	https://hub.docker.com/r/griffithlab/regtools/	NNP
10_1101-436634	358	23	)	)	-RRB-
10_1101-436634	358	24	.	.	.
10_1101-436634	359	1	This	this	DT
10_1101-436634	359	2	Docker	Docker	NNP
10_1101-436634	359	3	container	container	NN
10_1101-436634	359	4	allows	allow	VBZ
10_1101-436634	359	5	a	a	DT
10_1101-436634	359	6	user	user	NN
10_1101-436634	359	7	to	to	TO
10_1101-436634	359	8	run	run	VB
10_1101-436634	359	9	the	the	DT
10_1101-436634	359	10	workflow	workflow	NN
10_1101-436634	359	11	we	-PRON-	PRP
10_1101-436634	359	12	outline	outline	VBP
10_1101-436634	359	13	at	at	IN
10_1101-436634	359	14	https://regtools.readthedocs.io/en/latest/workflow/.	https://regtools.readthedocs.io/en/latest/workflow/.	NNP
10_1101-436634	360	1	Docker	Docker	NNP
10_1101-436634	360	2	is	be	VBZ
10_1101-436634	360	3	an	an	DT
10_1101-436634	360	4	open-	open-	JJ
10_1101-436634	360	5	source	source	NN
10_1101-436634	360	6	software	software	NN
10_1101-436634	360	7	platform	platform	NN
10_1101-436634	360	8	that	that	WDT
10_1101-436634	360	9	enables	enable	VBZ
10_1101-436634	360	10	applications	application	NNS
10_1101-436634	360	11	to	to	TO
10_1101-436634	360	12	be	be	VB
10_1101-436634	360	13	readily	readily	RB
10_1101-436634	360	14	installed	instal	VBN
10_1101-436634	360	15	and	and	CC
10_1101-436634	360	16	run	run	VBN
10_1101-436634	360	17	on	on	IN
10_1101-436634	360	18	any	any	DT
10_1101-436634	360	19	system	system	NN
10_1101-436634	360	20	.	.	.
10_1101-436634	361	1	The	the	DT
10_1101-436634	361	2	availability	availability	NN
10_1101-436634	361	3	of	of	IN
10_1101-436634	361	4	RegTools	RegTools	NNP
10_1101-436634	361	5	with	with	IN
10_1101-436634	361	6	all	all	PDT
10_1101-436634	361	7	its	-PRON-	PRP$
10_1101-436634	361	8	dependencies	dependency	NNS
10_1101-436634	361	9	as	as	IN
10_1101-436634	361	10	a	a	DT
10_1101-436634	361	11	Docker	Docker	NNP
10_1101-436634	361	12	container	container	NN
10_1101-436634	361	13	also	also	RB
10_1101-436634	361	14	facilitates	facilitate	VBZ
10_1101-436634	361	15	the	the	DT
10_1101-436634	361	16	integration	integration	NN
10_1101-436634	361	17	of	of	IN
10_1101-436634	361	18	the	the	DT
10_1101-436634	361	19	RegTools	RegTools	NNP
10_1101-436634	361	20	software	software	NN
10_1101-436634	361	21	into	into	IN
10_1101-436634	361	22	workflow	workflow	NN
10_1101-436634	361	23	pipelines	pipeline	NNS
10_1101-436634	361	24	that	that	WDT
10_1101-436634	361	25	support	support	VBP
10_1101-436634	361	26	Docker	Docker	NNP
10_1101-436634	361	27	images	image	NNS
10_1101-436634	361	28	.	.	.
10_1101-436634	362	1	Data	datum	NNS
10_1101-436634	362	2	availability	availability	NN
10_1101-436634	362	3	Sequence	Sequence	NNP
10_1101-436634	362	4	data	datum	NNS
10_1101-436634	362	5	for	for	IN
10_1101-436634	362	6	each	each	DT
10_1101-436634	362	7	cohort	cohort	NN
10_1101-436634	362	8	analyzed	analyze	VBN
10_1101-436634	362	9	in	in	IN
10_1101-436634	362	10	this	this	DT
10_1101-436634	362	11	study	study	NN
10_1101-436634	362	12	are	be	VBP
10_1101-436634	362	13	available	available	JJ
10_1101-436634	362	14	through	through	IN
10_1101-436634	362	15	dbGaP	dbgap	NN
10_1101-436634	362	16	at	at	IN
10_1101-436634	362	17	the	the	DT
10_1101-436634	362	18	following	follow	VBG
10_1101-436634	362	19	accession	accession	NN
10_1101-436634	362	20	IDs	id	NNS
10_1101-436634	362	21	:	:	:
10_1101-436634	362	22	phs000178	phs000178	NN
10_1101-436634	362	23	for	for	IN
10_1101-436634	362	24	TCGA	TCGA	NNP
10_1101-436634	362	25	cohorts	cohort	NNS
10_1101-436634	362	26	,	,	,
10_1101-436634	362	27	phs001106	phs001106	NNP
10_1101-436634	362	28	for	for	IN
10_1101-436634	362	29	HCC	HCC	NNP
10_1101-436634	362	30	,	,	,
10_1101-436634	362	31	phs001049	phs001049	NNP
10_1101-436634	362	32	for	for	IN
10_1101-436634	362	33	SCLC	SCLC	NNP
10_1101-436634	362	34	,	,	,
10_1101-436634	362	35	and	and	CC
10_1101-436634	362	36	phs001623	phs001623	NNP
10_1101-436634	362	37	for	for	IN
10_1101-436634	362	38	OSCC	OSCC	NNP
10_1101-436634	362	39	.	.	.
10_1101-436634	363	1	Statistically	statistically	RB
10_1101-436634	363	2	significant	significant	JJ
10_1101-436634	363	3	events	event	NNS
10_1101-436634	363	4	for	for	IN
10_1101-436634	363	5	D	d	NN
10_1101-436634	363	6	,	,	,
10_1101-436634	363	7	A	a	NN
10_1101-436634	363	8	,	,	,
10_1101-436634	363	9	and	and	CC
10_1101-436634	363	10	NDA	NDA	NNP
10_1101-436634	363	11	junctions	junction	NNS
10_1101-436634	363	12	across	across	IN
10_1101-436634	363	13	the	the	DT
10_1101-436634	363	14	four	four	CD
10_1101-436634	363	15	variant	variant	JJ
10_1101-436634	363	16	splicing	splicing	NN
10_1101-436634	363	17	windows	window	NNS
10_1101-436634	363	18	used	use	VBN
10_1101-436634	363	19	are	be	VBP
10_1101-436634	363	20	available	available	JJ
10_1101-436634	363	21	via	via	IN
10_1101-436634	363	22	Supplemental	Supplemental	NNP
10_1101-436634	363	23	Files	Files	NNP
10_1101-436634	363	24	1	1	CD
10_1101-436634	363	25	and	and	CC
10_1101-436634	363	26	2	2	CD
10_1101-436634	363	27	.	.	.
10_1101-436634	364	1	Statistically	statistically	RB
10_1101-436634	364	2	significant	significant	JJ
10_1101-436634	364	3	events	event	NNS
10_1101-436634	364	4	for	for	IN
10_1101-436634	364	5	DA	DA	NNP
10_1101-436634	364	6	junctions	junction	NNS
10_1101-436634	364	7	are	be	VBP
10_1101-436634	364	8	available	available	JJ
10_1101-436634	364	9	as	as	IN
10_1101-436634	364	10	Supplemental	Supplemental	NNP
10_1101-436634	364	11	Files	Files	NNP
10_1101-436634	364	12	3	3	CD
10_1101-436634	364	13	and	and	CC
10_1101-436634	364	14	4	4	CD
10_1101-436634	364	15	.	.	.
10_1101-436634	365	1	Complete	complete	JJ
10_1101-436634	365	2	results	result	NNS
10_1101-436634	365	3	of	of	IN
10_1101-436634	365	4	gene	gene	NN
10_1101-436634	365	5	recurrence	recurrence	NN
10_1101-436634	365	6	analysis	analysis	NN
10_1101-436634	365	7	are	be	VBP
10_1101-436634	365	8	available	available	JJ
10_1101-436634	365	9	as	as	IN
10_1101-436634	365	10	Supplemental	Supplemental	NNP
10_1101-436634	365	11	Files	Files	NNP
10_1101-436634	365	12	5	5	CD
10_1101-436634	365	13	and	and	CC
10_1101-436634	365	14	6	6	CD
10_1101-436634	365	15	.	.	.
10_1101-436634	366	1	Acknowledgments	acknowledgment	NNS
10_1101-436634	366	2	We	-PRON-	PRP
10_1101-436634	366	3	thank	thank	VBP
10_1101-436634	366	4	the	the	DT
10_1101-436634	366	5	patients	patient	NNS
10_1101-436634	366	6	and	and	CC
10_1101-436634	366	7	their	-PRON-	PRP$
10_1101-436634	366	8	families	family	NNS
10_1101-436634	366	9	for	for	IN
10_1101-436634	366	10	donation	donation	NN
10_1101-436634	366	11	of	of	IN
10_1101-436634	366	12	their	-PRON-	PRP$
10_1101-436634	366	13	samples	sample	NNS
10_1101-436634	366	14	and	and	CC
10_1101-436634	366	15	participation	participation	NN
10_1101-436634	366	16	in	in	IN
10_1101-436634	366	17	clinical	clinical	JJ
10_1101-436634	366	18	trials	trial	NNS
10_1101-436634	366	19	.	.	.
10_1101-436634	367	1	We	-PRON-	PRP
10_1101-436634	367	2	would	would	MD
10_1101-436634	367	3	like	like	VB
10_1101-436634	367	4	to	to	TO
10_1101-436634	367	5	thank	thank	VB
10_1101-436634	367	6	Donald	Donald	NNP
10_1101-436634	367	7	Conrad	Conrad	NNP
10_1101-436634	367	8	for	for	IN
10_1101-436634	367	9	his	-PRON-	PRP$
10_1101-436634	367	10	initial	initial	JJ
10_1101-436634	367	11	idea	idea	NN
10_1101-436634	367	12	to	to	TO
10_1101-436634	367	13	compare	compare	VB
10_1101-436634	367	14	to	to	IN
10_1101-436634	367	15	variant	variant	JJ
10_1101-436634	367	16	effect	effect	NN
10_1101-436634	367	17	predictor	predictor	NN
10_1101-436634	367	18	tools	tool	NNS
10_1101-436634	367	19	.	.	.
10_1101-436634	368	1	Kelsy	Kelsy	NNP
10_1101-436634	368	2	Cotto	Cotto	NNP
10_1101-436634	368	3	was	be	VBD
10_1101-436634	368	4	supported	support	VBN
10_1101-436634	368	5	by	by	IN
10_1101-436634	368	6	Siteman	Siteman	NNP
10_1101-436634	368	7	Cancer	Cancer	NNP
10_1101-436634	368	8	Center	Center	NNP
10_1101-436634	368	9	under	under	IN
10_1101-436634	368	10	fund	fund	NN
10_1101-436634	368	11	number	number	NN
10_1101-436634	368	12	#	#	$
10_1101-436634	368	13	3477	3477	CD
10_1101-436634	368	14	-	-	SYM
10_1101-436634	368	15	92400	92400	CD
10_1101-436634	368	16	and	and	CC
10_1101-436634	368	17	T32CA113275	T32CA113275	NNP
10_1101-436634	368	18	.	.	.
10_1101-436634	369	1	Avinash	Avinash	NNP
10_1101-436634	369	2	Ramu	Ramu	NNP
10_1101-436634	369	3	was	be	VBD
10_1101-436634	369	4	supported	support	VBN
10_1101-436634	369	5	by	by	IN
10_1101-436634	369	6	the	the	DT
10_1101-436634	369	7	‘	'	``
10_1101-436634	369	8	Burroughs	Burroughs	NNP
10_1101-436634	369	9	Wellcome	Wellcome	NNP
10_1101-436634	369	10	Fund	Fund	NNP
10_1101-436634	369	11	Institutional	Institutional	NNP
10_1101-436634	369	12	Program	Program	NNP
10_1101-436634	369	13	Unifying	Unifying	NNP
10_1101-436634	369	14	Population	Population	NNP
10_1101-436634	369	15	and	and	CC
10_1101-436634	369	16	Laboratory	Laboratory	NNP
10_1101-436634	369	17	Based	Based	NNP
10_1101-436634	369	18	Sciences	Sciences	NNPS
10_1101-436634	369	19	Award	Award	NNP
10_1101-436634	369	20	’	'	''
10_1101-436634	369	21	at	at	IN
10_1101-436634	369	22	Washington	Washington	NNP
10_1101-436634	369	23	University	University	NNP
10_1101-436634	369	24	.	.	.
10_1101-436634	370	1	Malachi	Malachi	NNP
10_1101-436634	370	2	Griffith	Griffith	NNP
10_1101-436634	370	3	was	be	VBD
10_1101-436634	370	4	supported	support	VBN
10_1101-436634	370	5	by	by	IN
10_1101-436634	370	6	the	the	DT
10_1101-436634	370	7	National	National	NNP
10_1101-436634	370	8	Human	Human	NNP
10_1101-436634	370	9	Genome	Genome	NNP
10_1101-436634	370	10	Research	Research	NNP
10_1101-436634	370	11	Institute	Institute	NNP
10_1101-436634	370	12	(	(	-LRB-
10_1101-436634	370	13	NHGRI	NHGRI	NNP
10_1101-436634	370	14	)	)	-RRB-
10_1101-436634	370	15	of	of	IN
10_1101-436634	370	16	the	the	DT
10_1101-436634	370	17	National	National	NNP
10_1101-436634	370	18	Institutes	Institutes	NNPS
10_1101-436634	370	19	of	of	IN
10_1101-436634	370	20	Health	Health	NNP
10_1101-436634	370	21	(	(	-LRB-
10_1101-436634	370	22	NIH	NIH	NNP
10_1101-436634	370	23	)	)	-RRB-
10_1101-436634	370	24	under	under	IN
10_1101-436634	370	25	Award	Award	NNP
10_1101-436634	370	26	Number	Number	NNP
10_1101-436634	370	27	R00HG007940	R00HG007940	NNP
10_1101-436634	370	28	.	.	.
10_1101-436634	371	1	Malachi	Malachi	NNP
10_1101-436634	371	2	Griffith	Griffith	NNP
10_1101-436634	371	3	and	and	CC
10_1101-436634	371	4	Obi	Obi	NNP
10_1101-436634	371	5	Griffith	Griffith	NNP
10_1101-436634	371	6	were	be	VBD
10_1101-436634	371	7	supported	support	VBN
10_1101-436634	371	8	by	by	IN
10_1101-436634	371	9	the	the	DT
10_1101-436634	371	10	NIH	NIH	NNP
10_1101-436634	371	11	National	National	NNP
10_1101-436634	371	12	Cancer	Cancer	NNP
10_1101-436634	371	13	Institute	Institute	NNP
10_1101-436634	371	14	(	(	-LRB-
10_1101-436634	371	15	NCI	NCI	NNP
10_1101-436634	371	16	)	)	-RRB-
10_1101-436634	371	17	under	under	IN
10_1101-436634	371	18	Award	Award	NNP
10_1101-436634	371	19	Numbers	Numbers	NNPS
10_1101-436634	371	20	U01CA209936	U01CA209936	NNP
10_1101-436634	371	21	,	,	,
10_1101-436634	371	22	U01CA231844	U01CA231844	NNP
10_1101-436634	371	23	,	,	,
10_1101-436634	371	24	U01CA248235	U01CA248235	NNP
10_1101-436634	371	25	U24CA237719	U24CA237719	NNP
10_1101-436634	371	26	.	.	.
10_1101-436634	372	1	Malachi	Malachi	NNP
10_1101-436634	372	2	Griffith	Griffith	NNP
10_1101-436634	372	3	and	and	CC
10_1101-436634	372	4	Megan	Megan	NNP
10_1101-436634	372	5	Richters	Richters	NNPS
10_1101-436634	372	6	were	be	VBD
10_1101-436634	372	7	supported	support	VBN
10_1101-436634	372	8	by	by	IN
10_1101-436634	372	9	the	the	DT
10_1101-436634	372	10	V	V	NNP
10_1101-436634	372	11	Foundation	Foundation	NNP
10_1101-436634	372	12	for	for	IN
10_1101-436634	372	13	Cancer	Cancer	NNP
10_1101-436634	372	14	Research	Research	NNP
10_1101-436634	372	15	under	under	IN
10_1101-436634	372	16	Award	Award	NNP
10_1101-436634	372	17	Number	Number	NNP
10_1101-436634	372	18	V2018	V2018	NNP
10_1101-436634	372	19	-	-	HYPH
10_1101-436634	372	20	007	007	CD
10_1101-436634	372	21	.	.	.
10_1101-436634	373	1	The	the	DT
10_1101-436634	373	2	results	result	NNS
10_1101-436634	373	3	published	publish	VBN
10_1101-436634	373	4	here	here	RB
10_1101-436634	373	5	are	be	VBP
10_1101-436634	373	6	in	in	IN
10_1101-436634	373	7	whole	whole	JJ
10_1101-436634	373	8	or	or	CC
10_1101-436634	373	9	part	part	NN
10_1101-436634	373	10	based	base	VBN
10_1101-436634	373	11	upon	upon	IN
10_1101-436634	373	12	data	datum	NNS
10_1101-436634	373	13	generated	generate	VBN
10_1101-436634	373	14	by	by	IN
10_1101-436634	373	15	the	the	DT
10_1101-436634	373	16	TCGA	TCGA	NNP
10_1101-436634	373	17	Research	Research	NNP
10_1101-436634	373	18	Network	Network	NNP
10_1101-436634	373	19	:	:	:
10_1101-436634	373	20	https://www.cancer.gov/tcga	https://www.cancer.gov/tcga	ADD
10_1101-436634	373	21	.	.	.
10_1101-436634	374	1	Contributions	Contributions	NNP
10_1101-436634	374	2	K.C.C.	K.C.C.	NNP
10_1101-436634	375	1	and	and	CC
10_1101-436634	375	2	Y.-Y.F.	Y.-Y.F.	NNP
10_1101-436634	376	1	were	be	VBD
10_1101-436634	376	2	involved	involve	VBN
10_1101-436634	376	3	in	in	IN
10_1101-436634	376	4	all	all	DT
10_1101-436634	376	5	aspects	aspect	NNS
10_1101-436634	376	6	of	of	IN
10_1101-436634	376	7	this	this	DT
10_1101-436634	376	8	study	study	NN
10_1101-436634	376	9	,	,	,
10_1101-436634	376	10	including	include	VBG
10_1101-436634	376	11	designing	design	VBG
10_1101-436634	376	12	methodology	methodology	NN
10_1101-436634	376	13	,	,	,
10_1101-436634	376	14	developing	develop	VBG
10_1101-436634	376	15	and	and	CC
10_1101-436634	376	16	testing	test	VBG
10_1101-436634	376	17	the	the	DT
10_1101-436634	376	18	tool	tool	NN
10_1101-436634	376	19	software	software	NN
10_1101-436634	376	20	,	,	,
10_1101-436634	376	21	analyzing	analyze	VBG
10_1101-436634	376	22	and	and	CC
10_1101-436634	376	23	interpreting	interpret	VBG
10_1101-436634	376	24	data	datum	NNS
10_1101-436634	376	25	,	,	,
10_1101-436634	376	26	and	and	CC
10_1101-436634	376	27	writing	write	VBG
10_1101-436634	376	28	the	the	DT
10_1101-436634	376	29	.CC	.CC	NFP
10_1101-436634	376	30	-	-	HYPH
10_1101-436634	376	31	BY	by	IN
10_1101-436634	376	32	-	-	HYPH
10_1101-436634	376	33	NC	NC	NNP
10_1101-436634	376	34	-	-	HYPH
10_1101-436634	376	35	ND	ND	NNP
10_1101-436634	376	36	4.0	4.0	CD
10_1101-436634	376	37	International	international	JJ
10_1101-436634	376	38	licensea	licensea	NNS
10_1101-436634	376	39	certified	certify	VBN
10_1101-436634	376	40	by	by	IN
10_1101-436634	376	41	peer	peer	NN
10_1101-436634	376	42	review	review	NN
10_1101-436634	376	43	)	)	-RRB-
10_1101-436634	376	44	is	be	VBZ
10_1101-436634	376	45	the	the	DT
10_1101-436634	376	46	author	author	NN
10_1101-436634	376	47	/	/	SYM
10_1101-436634	376	48	funder	funder	NN
10_1101-436634	376	49	,	,	,
10_1101-436634	376	50	who	who	WP
10_1101-436634	376	51	has	have	VBZ
10_1101-436634	376	52	granted	grant	VBN
10_1101-436634	376	53	bioRxiv	biorxiv	IN
10_1101-436634	376	54	a	a	DT
10_1101-436634	376	55	license	license	NN
10_1101-436634	376	56	to	to	TO
10_1101-436634	376	57	display	display	VB
10_1101-436634	376	58	the	the	DT
10_1101-436634	376	59	preprint	preprint	NN
10_1101-436634	376	60	in	in	IN
10_1101-436634	376	61	perpetuity	perpetuity	NN
10_1101-436634	376	62	.	.	.
10_1101-436634	377	1	It	-PRON-	PRP
10_1101-436634	377	2	is	be	VBZ
10_1101-436634	377	3	made	make	VBN
10_1101-436634	377	4	available	available	JJ
10_1101-436634	377	5	under	under	IN
10_1101-436634	377	6	The	the	DT
10_1101-436634	377	7	copyright	copyright	NN
10_1101-436634	377	8	holder	holder	NN
10_1101-436634	377	9	for	for	IN
10_1101-436634	377	10	this	this	DT
10_1101-436634	377	11	preprint	preprint	NN
10_1101-436634	377	12	(	(	-LRB-
10_1101-436634	377	13	which	which	WDT
10_1101-436634	377	14	was	be	VBD
10_1101-436634	377	15	notthis	notthis	DT
10_1101-436634	377	16	version	version	NN
10_1101-436634	377	17	posted	post	VBN
10_1101-436634	377	18	January	January	NNP
10_1101-436634	377	19	5	5	CD
10_1101-436634	377	20	,	,	,
10_1101-436634	377	21	2021	2021	CD
10_1101-436634	377	22	.	.	.
10_1101-436634	377	23	;	;	:
10_1101-436634	377	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	377	25	:	:	:
10_1101-436634	377	26	bioRxiv	biorxiv	VB
10_1101-436634	377	27	preprint	preprint	NN
10_1101-436634	377	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	377	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	377	30	18	18	CD
10_1101-436634	377	31	manuscript	manuscript	NN
10_1101-436634	377	32	,	,	,
10_1101-436634	377	33	with	with	IN
10_1101-436634	377	34	input	input	NN
10_1101-436634	377	35	from	from	IN
10_1101-436634	377	36	A.R.	A.R.	NNP
10_1101-436634	377	37	,	,	,
10_1101-436634	377	38	Z.L.S.	Z.L.S.	NNP
10_1101-436634	377	39	,	,	,
10_1101-436634	377	40	M.R.	M.R.	NNP
10_1101-436634	377	41	,	,	,
10_1101-436634	377	42	S.F.	S.F.	NNP
10_1101-436634	377	43	,	,	,
10_1101-436634	377	44	J.K.	J.K.	NNP
10_1101-436634	377	45	,	,	,
10_1101-436634	377	46	O.L.G.	O.L.G.	NNP
10_1101-436634	377	47	,	,	,
10_1101-436634	377	48	and	and	CC
10_1101-436634	377	49	M.G.	M.G.	NNP
10_1101-436634	378	1	A.R.	A.R.	NNP
10_1101-436634	379	1	designed	design	VBD
10_1101-436634	379	2	the	the	DT
10_1101-436634	379	3	tool	tool	NN
10_1101-436634	379	4	and	and	CC
10_1101-436634	379	5	led	lead	VBN
10_1101-436634	379	6	software	software	NN
10_1101-436634	379	7	development	development	NN
10_1101-436634	379	8	efforts	effort	NNS
10_1101-436634	379	9	.	.	.
10_1101-436634	380	1	Y.L.	Y.L.	NNP
10_1101-436634	380	2	,	,	,
10_1101-436634	380	3	W.C.C.	W.C.C.	NNP
10_1101-436634	380	4	,	,	,
10_1101-436634	380	5	R.U.	R.U.	NNP
10_1101-436634	380	6	,	,	,
10_1101-436634	380	7	and	and	CC
10_1101-436634	380	8	R.G.	R.G.	NNP
10_1101-436634	381	1	provided	provide	VBD
10_1101-436634	381	2	unpublished	unpublished	JJ
10_1101-436634	381	3	tumor	tumor	NN
10_1101-436634	381	4	datasets	dataset	NNS
10_1101-436634	381	5	and	and	CC
10_1101-436634	381	6	provided	provide	VBD
10_1101-436634	381	7	critical	critical	JJ
10_1101-436634	381	8	feedback	feedback	NN
10_1101-436634	381	9	on	on	IN
10_1101-436634	381	10	the	the	DT
10_1101-436634	381	11	manuscript	manuscript	NN
10_1101-436634	381	12	.	.	.
10_1101-436634	382	1	O.L.G.	O.L.G.	NNP
10_1101-436634	383	1	and	and	CC
10_1101-436634	383	2	M.G.	M.G.	NNP
10_1101-436634	384	1	supervised	supervise	VBD
10_1101-436634	384	2	the	the	DT
10_1101-436634	384	3	study	study	NN
10_1101-436634	384	4	.	.	.
10_1101-436634	385	1	All	all	DT
10_1101-436634	385	2	authors	author	NNS
10_1101-436634	385	3	read	read	VBP
10_1101-436634	385	4	and	and	CC
10_1101-436634	385	5	approved	approve	VBD
10_1101-436634	385	6	the	the	DT
10_1101-436634	385	7	final	final	JJ
10_1101-436634	385	8	manuscript	manuscript	NN
10_1101-436634	385	9	.	.	.
10_1101-436634	386	1	Conflicts	conflict	NNS
10_1101-436634	386	2	of	of	IN
10_1101-436634	386	3	Interest	Interest	NNP
10_1101-436634	386	4	W.	W.	NNP
10_1101-436634	386	5	Chapman	Chapman	NNP
10_1101-436634	386	6	serves	serve	VBZ
10_1101-436634	386	7	on	on	IN
10_1101-436634	386	8	the	the	DT
10_1101-436634	386	9	advisory	advisory	JJ
10_1101-436634	386	10	board	board	NN
10_1101-436634	386	11	for	for	IN
10_1101-436634	386	12	Novartis	Novartis	NNP
10_1101-436634	386	13	Pharmaceutical	Pharmaceutical	NNP
10_1101-436634	386	14	and	and	CC
10_1101-436634	386	15	reports	report	VBZ
10_1101-436634	386	16	intellectual	intellectual	JJ
10_1101-436634	386	17	property	property	NN
10_1101-436634	386	18	with	with	IN
10_1101-436634	386	19	Pathfinder	Pathfinder	NNP
10_1101-436634	386	20	Therapeutics	Therapeutics	NNP
10_1101-436634	386	21	.	.	.
10_1101-436634	387	1	R.	R.	NNP
10_1101-436634	387	2	Uppaluri	Uppaluri	NNP
10_1101-436634	387	3	reports	report	VBZ
10_1101-436634	387	4	grants	grant	NNS
10_1101-436634	387	5	and	and	CC
10_1101-436634	387	6	personal	personal	JJ
10_1101-436634	387	7	fees	fee	NNS
10_1101-436634	387	8	from	from	IN
10_1101-436634	387	9	Merck	Merck	NNP
10_1101-436634	387	10	Inc.	Inc.	NNP
10_1101-436634	387	11	R.	R.	NNP
10_1101-436634	387	12	Govindan	Govindan	NNP
10_1101-436634	387	13	served	serve	VBD
10_1101-436634	387	14	as	as	IN
10_1101-436634	387	15	consultant	consultant	NN
10_1101-436634	387	16	for	for	IN
10_1101-436634	387	17	Horizon	Horizon	NNP
10_1101-436634	387	18	Pharmaceuticals	Pharmaceuticals	NNPS
10_1101-436634	387	19	and	and	CC
10_1101-436634	387	20	GenePlus	GenePlus	NNP
10_1101-436634	387	21	.	.	.
10_1101-436634	388	1	References	reference	NNS
10_1101-436634	388	2	1	1	CD
10_1101-436634	388	3	.	.	.
10_1101-436634	389	1	Chabot	Chabot	NNP
10_1101-436634	389	2	,	,	,
10_1101-436634	389	3	B.	B.	NNP
10_1101-436634	390	1	&	&	CC
10_1101-436634	390	2	Shkreta	Shkreta	NNP
10_1101-436634	390	3	,	,	,
10_1101-436634	390	4	L.	L.	NNP
10_1101-436634	390	5	Defective	Defective	NNP
10_1101-436634	390	6	control	control	NN
10_1101-436634	390	7	of	of	IN
10_1101-436634	390	8	pre	pre	JJ
10_1101-436634	390	9	-	-	JJ
10_1101-436634	390	10	messenger	messenger	JJ
10_1101-436634	390	11	RNA	RNA	NNP
10_1101-436634	390	12	splicing	splice	VBG
10_1101-436634	390	13	in	in	IN
10_1101-436634	390	14	human	human	JJ
10_1101-436634	390	15	disease	disease	NN
10_1101-436634	390	16	.	.	.
10_1101-436634	391	1	J.	J.	NNP
10_1101-436634	392	1	Cell	Cell	NNP
10_1101-436634	392	2	Biol	Biol	NNP
10_1101-436634	392	3	.	.	.
10_1101-436634	393	1	212	212	CD
10_1101-436634	393	2	,	,	,
10_1101-436634	393	3	13–27	13–27	CD
10_1101-436634	393	4	(	(	-LRB-
10_1101-436634	393	5	2016	2016	CD
10_1101-436634	393	6	)	)	-RRB-
10_1101-436634	393	7	.	.	.
10_1101-436634	394	1	2	2	LS
10_1101-436634	394	2	.	.	.
10_1101-436634	395	1	Vogelstein	Vogelstein	NNP
10_1101-436634	395	2	,	,	,
10_1101-436634	395	3	B.	B.	NNP
10_1101-436634	395	4	et	et	NNP
10_1101-436634	395	5	al	al	NNP
10_1101-436634	395	6	.	.	.
10_1101-436634	396	1	Cancer	cancer	NN
10_1101-436634	396	2	genome	genome	NN
10_1101-436634	396	3	landscapes	landscape	NNS
10_1101-436634	396	4	.	.	.
10_1101-436634	397	1	Science	science	NN
10_1101-436634	397	2	339	339	CD
10_1101-436634	397	3	,	,	,
10_1101-436634	397	4	1546–1558	1546–1558	CD
10_1101-436634	397	5	(	(	-LRB-
10_1101-436634	397	6	2013	2013	CD
10_1101-436634	397	7	)	)	-RRB-
10_1101-436634	397	8	.	.	.
10_1101-436634	398	1	3	3	LS
10_1101-436634	398	2	.	.	.
10_1101-436634	399	1	Soemedi	Soemedi	NNP
10_1101-436634	399	2	,	,	,
10_1101-436634	399	3	R.	R.	NNP
10_1101-436634	399	4	et	et	NNP
10_1101-436634	399	5	al	al	NNP
10_1101-436634	399	6	.	.	.
10_1101-436634	400	1	Pathogenic	pathogenic	JJ
10_1101-436634	400	2	variants	variant	NNS
10_1101-436634	400	3	that	that	WDT
10_1101-436634	400	4	alter	alter	VBP
10_1101-436634	400	5	protein	protein	NN
10_1101-436634	400	6	code	code	NN
10_1101-436634	400	7	often	often	RB
10_1101-436634	400	8	disrupt	disrupt	VBP
10_1101-436634	400	9	splicing	splice	VBG
10_1101-436634	400	10	.	.	.
10_1101-436634	401	1	Nat	Nat	NNP
10_1101-436634	401	2	.	.	.
10_1101-436634	402	1	Genet	Genet	NNP
10_1101-436634	402	2	.	.	.
10_1101-436634	403	1	49	49	CD
10_1101-436634	403	2	,	,	,
10_1101-436634	403	3	848–855	848–855	CD
10_1101-436634	403	4	(	(	-LRB-
10_1101-436634	403	5	2017	2017	CD
10_1101-436634	403	6	)	)	-RRB-
10_1101-436634	403	7	.	.	.
10_1101-436634	404	1	4	4	LS
10_1101-436634	404	2	.	.	.
10_1101-436634	405	1	Supek	Supek	NNP
10_1101-436634	405	2	,	,	,
10_1101-436634	405	3	F.	F.	NNP
10_1101-436634	405	4	,	,	,
10_1101-436634	405	5	Miñana	Miñana	NNP
10_1101-436634	405	6	,	,	,
10_1101-436634	405	7	B.	B.	NNP
10_1101-436634	405	8	,	,	,
10_1101-436634	405	9	Valcárcel	Valcárcel	NNP
10_1101-436634	405	10	,	,	,
10_1101-436634	405	11	J.	J.	NNP
10_1101-436634	405	12	,	,	,
10_1101-436634	405	13	Gabaldón	Gabaldón	NNP
10_1101-436634	405	14	,	,	,
10_1101-436634	405	15	T.	T.	NNP
10_1101-436634	405	16	&	&	CC
10_1101-436634	405	17	Lehner	Lehner	NNP
10_1101-436634	405	18	,	,	,
10_1101-436634	405	19	B.	B.	NNP
10_1101-436634	405	20	Synonymous	synonymous	JJ
10_1101-436634	405	21	mutations	mutation	NNS
10_1101-436634	405	22	frequently	frequently	RB
10_1101-436634	405	23	act	act	VBP
10_1101-436634	405	24	as	as	IN
10_1101-436634	405	25	driver	driver	NN
10_1101-436634	405	26	mutations	mutation	NNS
10_1101-436634	405	27	in	in	IN
10_1101-436634	405	28	human	human	JJ
10_1101-436634	405	29	cancers	cancer	NNS
10_1101-436634	405	30	.	.	.
10_1101-436634	406	1	Cell	Cell	NNP
10_1101-436634	406	2	156	156	CD
10_1101-436634	406	3	,	,	,
10_1101-436634	406	4	1324–1335	1324–1335	CD
10_1101-436634	406	5	(	(	-LRB-
10_1101-436634	406	6	2014	2014	CD
10_1101-436634	406	7	)	)	-RRB-
10_1101-436634	406	8	.	.	.
10_1101-436634	407	1	5	5	CD
10_1101-436634	407	2	.	.	.
10_1101-436634	408	1	Jung	Jung	NNP
10_1101-436634	408	2	,	,	,
10_1101-436634	408	3	H.	H.	NNP
10_1101-436634	408	4	et	et	NNP
10_1101-436634	408	5	al	al	NNP
10_1101-436634	408	6	.	.	.
10_1101-436634	409	1	Intron	Intron	NNP
10_1101-436634	409	2	retention	retention	NN
10_1101-436634	409	3	is	be	VBZ
10_1101-436634	409	4	a	a	DT
10_1101-436634	409	5	widespread	widespread	JJ
10_1101-436634	409	6	mechanism	mechanism	NN
10_1101-436634	409	7	of	of	IN
10_1101-436634	409	8	tumor	tumor	NN
10_1101-436634	409	9	-	-	HYPH
10_1101-436634	409	10	suppressor	suppressor	NN
10_1101-436634	409	11	inactivation	inactivation	NN
10_1101-436634	409	12	.	.	.
10_1101-436634	410	1	Nat	Nat	NNP
10_1101-436634	410	2	.	.	.
10_1101-436634	411	1	Genet	Genet	NNP
10_1101-436634	411	2	.	.	.
10_1101-436634	412	1	47	47	CD
10_1101-436634	412	2	,	,	,
10_1101-436634	412	3	1242–1248	1242–1248	CD
10_1101-436634	412	4	(	(	-LRB-
10_1101-436634	412	5	2015	2015	CD
10_1101-436634	412	6	)	)	-RRB-
10_1101-436634	412	7	.	.	.
10_1101-436634	413	1	6	6	CD
10_1101-436634	413	2	.	.	.
10_1101-436634	414	1	Venables	Venables	NNP
10_1101-436634	414	2	,	,	,
10_1101-436634	414	3	J.	J.	NNP
10_1101-436634	414	4	P.	P.	NNP
10_1101-436634	414	5	Aberrant	Aberrant	NNP
10_1101-436634	414	6	and	and	CC
10_1101-436634	414	7	alternative	alternative	JJ
10_1101-436634	414	8	splicing	splicing	NN
10_1101-436634	414	9	in	in	IN
10_1101-436634	414	10	cancer	cancer	NN
10_1101-436634	414	11	.	.	.
10_1101-436634	415	1	Cancer	cancer	NN
10_1101-436634	415	2	Res	Res	NNP
10_1101-436634	415	3	.	.	.
10_1101-436634	416	1	64	64	CD
10_1101-436634	416	2	,	,	,
10_1101-436634	416	3	7647–7654	7647–7654	CD
10_1101-436634	416	4	(	(	-LRB-
10_1101-436634	416	5	2004	2004	CD
10_1101-436634	416	6	)	)	-RRB-
10_1101-436634	416	7	.	.	.
10_1101-436634	417	1	7	7	LS
10_1101-436634	417	2	.	.	.
10_1101-436634	418	1	Climente	Climente	NNP
10_1101-436634	418	2	-	-	HYPH
10_1101-436634	418	3	González	González	NNP
10_1101-436634	418	4	,	,	,
10_1101-436634	418	5	H.	H.	NNP
10_1101-436634	418	6	,	,	,
10_1101-436634	418	7	Porta	Porta	NNP
10_1101-436634	418	8	-	-	HYPH
10_1101-436634	418	9	Pardo	Pardo	NNP
10_1101-436634	418	10	,	,	,
10_1101-436634	418	11	E.	E.	NNP
10_1101-436634	418	12	,	,	,
10_1101-436634	418	13	Godzik	Godzik	NNP
10_1101-436634	418	14	,	,	,
10_1101-436634	418	15	A.	a.	NN
10_1101-436634	419	1	&	&	CC
10_1101-436634	419	2	Eyras	Eyras	NNP
10_1101-436634	419	3	,	,	,
10_1101-436634	419	4	E.	E.	NNP
10_1101-436634	419	5	The	the	DT
10_1101-436634	419	6	Functional	Functional	NNP
10_1101-436634	419	7	Impact	Impact	NNP
10_1101-436634	419	8	of	of	IN
10_1101-436634	419	9	Alternative	Alternative	NNP
10_1101-436634	419	10	Splicing	Splicing	NNP
10_1101-436634	419	11	in	in	IN
10_1101-436634	419	12	Cancer	Cancer	NNP
10_1101-436634	419	13	.	.	.
10_1101-436634	420	1	Cell	Cell	NNP
10_1101-436634	420	2	Rep.	Rep.	NNP
10_1101-436634	420	3	20	20	CD
10_1101-436634	420	4	,	,	,
10_1101-436634	420	5	2215–2226	2215–2226	CD
10_1101-436634	420	6	(	(	-LRB-
10_1101-436634	420	7	2017	2017	CD
10_1101-436634	420	8	)	)	-RRB-
10_1101-436634	420	9	.	.	.
10_1101-436634	421	1	8	8	LS
10_1101-436634	421	2	.	.	.
10_1101-436634	422	1	Chen	Chen	NNP
10_1101-436634	422	2	,	,	,
10_1101-436634	422	3	J.	J.	NNP
10_1101-436634	423	1	&	&	CC
10_1101-436634	423	2	Weiss	Weiss	NNP
10_1101-436634	423	3	,	,	,
10_1101-436634	423	4	W.	W.	NNP
10_1101-436634	423	5	A.	A.	NNP
10_1101-436634	424	1	Alternative	alternative	JJ
10_1101-436634	424	2	splicing	splicing	NN
10_1101-436634	424	3	in	in	IN
10_1101-436634	424	4	cancer	cancer	NN
10_1101-436634	424	5	:	:	:
10_1101-436634	424	6	implications	implication	NNS
10_1101-436634	424	7	for	for	IN
10_1101-436634	424	8	biology	biology	NN
10_1101-436634	424	9	and	and	CC
10_1101-436634	424	10	therapy	therapy	NN
10_1101-436634	424	11	.	.	.
10_1101-436634	425	1	Oncogene	oncogene	NN
10_1101-436634	425	2	34	34	CD
10_1101-436634	425	3	,	,	,
10_1101-436634	425	4	1–14	1–14	CD
10_1101-436634	425	5	(	(	-LRB-
10_1101-436634	425	6	2015	2015	CD
10_1101-436634	425	7	)	)	-RRB-
10_1101-436634	425	8	.	.	.
10_1101-436634	426	1	9	9	CD
10_1101-436634	426	2	.	.	.
10_1101-436634	427	1	Xiong	Xiong	NNP
10_1101-436634	427	2	,	,	,
10_1101-436634	427	3	H.	H.	NNP
10_1101-436634	427	4	Y.	Y.	NNP
10_1101-436634	427	5	et	et	NNP
10_1101-436634	427	6	al	al	NNP
10_1101-436634	427	7	.	.	.
10_1101-436634	428	1	RNA	RNA	NNP
10_1101-436634	428	2	splicing	splice	VBG
10_1101-436634	428	3	.	.	.
10_1101-436634	429	1	The	the	DT
10_1101-436634	429	2	human	human	JJ
10_1101-436634	429	3	splicing	splicing	NN
10_1101-436634	429	4	code	code	NN
10_1101-436634	429	5	reveals	reveal	VBZ
10_1101-436634	429	6	new	new	JJ
10_1101-436634	429	7	insights	insight	NNS
10_1101-436634	429	8	into	into	IN
10_1101-436634	429	9	the	the	DT
10_1101-436634	429	10	genetic	genetic	JJ
10_1101-436634	429	11	determinants	determinant	NNS
10_1101-436634	429	12	of	of	IN
10_1101-436634	429	13	disease	disease	NN
10_1101-436634	429	14	.	.	.
10_1101-436634	430	1	Science	science	NN
10_1101-436634	430	2	347	347	CD
10_1101-436634	430	3	,	,	,
10_1101-436634	430	4	1254806	1254806	CD
10_1101-436634	430	5	(	(	-LRB-
10_1101-436634	430	6	2015	2015	CD
10_1101-436634	430	7	)	)	-RRB-
10_1101-436634	430	8	.	.	.
10_1101-436634	431	1	10	10	CD
10_1101-436634	431	2	.	.	.
10_1101-436634	432	1	Yeo	Yeo	NNP
10_1101-436634	432	2	,	,	,
10_1101-436634	432	3	G.	G.	NNP
10_1101-436634	432	4	&	&	CC
10_1101-436634	432	5	Burge	Burge	NNP
10_1101-436634	432	6	,	,	,
10_1101-436634	432	7	C.	C.	NNP
10_1101-436634	432	8	B.	B.	NNP
10_1101-436634	433	1	Maximum	maximum	JJ
10_1101-436634	433	2	entropy	entropy	JJ
10_1101-436634	433	3	modeling	modeling	NN
10_1101-436634	433	4	of	of	IN
10_1101-436634	433	5	short	short	JJ
10_1101-436634	433	6	sequence	sequence	NN
10_1101-436634	433	7	motifs	motif	NNS
10_1101-436634	433	8	with	with	IN
10_1101-436634	433	9	applications	application	NNS
10_1101-436634	433	10	to	to	TO
10_1101-436634	433	11	RNA	rna	VB
10_1101-436634	433	12	splicing	splicing	NN
10_1101-436634	433	13	signals	signal	NNS
10_1101-436634	433	14	.	.	.
10_1101-436634	434	1	J.	J.	NNP
10_1101-436634	434	2	Comput	Comput	NNP
10_1101-436634	434	3	.	.	.
10_1101-436634	435	1	Biol	Biol	NNP
10_1101-436634	435	2	.	.	.
10_1101-436634	436	1	11	11	CD
10_1101-436634	436	2	,	,	,
10_1101-436634	436	3	377–394	377–394	CD
10_1101-436634	436	4	(	(	-LRB-
10_1101-436634	436	5	2004	2004	CD
10_1101-436634	436	6	)	)	-RRB-
10_1101-436634	436	7	.	.	.
10_1101-436634	437	1	.CC	.CC	NFP
10_1101-436634	437	2	-	-	:
10_1101-436634	437	3	BY	by	IN
10_1101-436634	437	4	-	-	HYPH
10_1101-436634	437	5	NC	NC	NNP
10_1101-436634	437	6	-	-	HYPH
10_1101-436634	437	7	ND	ND	NNP
10_1101-436634	437	8	4.0	4.0	CD
10_1101-436634	437	9	International	international	JJ
10_1101-436634	437	10	licensea	licensea	NNS
10_1101-436634	437	11	certified	certify	VBN
10_1101-436634	437	12	by	by	IN
10_1101-436634	437	13	peer	peer	NN
10_1101-436634	437	14	review	review	NN
10_1101-436634	437	15	)	)	-RRB-
10_1101-436634	437	16	is	be	VBZ
10_1101-436634	437	17	the	the	DT
10_1101-436634	437	18	author	author	NN
10_1101-436634	437	19	/	/	SYM
10_1101-436634	437	20	funder	funder	NN
10_1101-436634	437	21	,	,	,
10_1101-436634	437	22	who	who	WP
10_1101-436634	437	23	has	have	VBZ
10_1101-436634	437	24	granted	grant	VBN
10_1101-436634	437	25	bioRxiv	biorxiv	IN
10_1101-436634	437	26	a	a	DT
10_1101-436634	437	27	license	license	NN
10_1101-436634	437	28	to	to	TO
10_1101-436634	437	29	display	display	VB
10_1101-436634	437	30	the	the	DT
10_1101-436634	437	31	preprint	preprint	NN
10_1101-436634	437	32	in	in	IN
10_1101-436634	437	33	perpetuity	perpetuity	NN
10_1101-436634	437	34	.	.	.
10_1101-436634	438	1	It	-PRON-	PRP
10_1101-436634	438	2	is	be	VBZ
10_1101-436634	438	3	made	make	VBN
10_1101-436634	438	4	available	available	JJ
10_1101-436634	438	5	under	under	IN
10_1101-436634	438	6	The	the	DT
10_1101-436634	438	7	copyright	copyright	NN
10_1101-436634	438	8	holder	holder	NN
10_1101-436634	438	9	for	for	IN
10_1101-436634	438	10	this	this	DT
10_1101-436634	438	11	preprint	preprint	NN
10_1101-436634	438	12	(	(	-LRB-
10_1101-436634	438	13	which	which	WDT
10_1101-436634	438	14	was	be	VBD
10_1101-436634	438	15	notthis	notthis	DT
10_1101-436634	438	16	version	version	NN
10_1101-436634	438	17	posted	post	VBN
10_1101-436634	438	18	January	January	NNP
10_1101-436634	438	19	5	5	CD
10_1101-436634	438	20	,	,	,
10_1101-436634	438	21	2021	2021	CD
10_1101-436634	438	22	.	.	.
10_1101-436634	438	23	;	;	:
10_1101-436634	438	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	438	25	:	:	:
10_1101-436634	438	26	bioRxiv	biorxiv	VB
10_1101-436634	438	27	preprint	preprint	NN
10_1101-436634	438	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	438	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	CD
10_1101-436634	438	30	19	19	CD
10_1101-436634	438	31	11	11	CD
10_1101-436634	438	32	.	.	.
10_1101-436634	439	1	Fairbrother	fairbrother	RB
10_1101-436634	439	2	,	,	,
10_1101-436634	439	3	W.	W.	NNP
10_1101-436634	439	4	G.	G.	NNP
10_1101-436634	439	5	,	,	,
10_1101-436634	439	6	Yeh	Yeh	NNP
10_1101-436634	439	7	,	,	,
10_1101-436634	439	8	R.-F.	R.-F.	NNP
10_1101-436634	439	9	,	,	,
10_1101-436634	439	10	Sharp	Sharp	NNP
10_1101-436634	439	11	,	,	,
10_1101-436634	439	12	P.	P.	NNP
10_1101-436634	439	13	A.	a.	NN
10_1101-436634	440	1	&	&	CC
10_1101-436634	440	2	Burge	Burge	NNP
10_1101-436634	440	3	,	,	,
10_1101-436634	440	4	C.	C.	NNP
10_1101-436634	440	5	B.	B.	NNP
10_1101-436634	440	6	Predictive	Predictive	NNP
10_1101-436634	440	7	identification	identification	NN
10_1101-436634	440	8	of	of	IN
10_1101-436634	440	9	exonic	exonic	JJ
10_1101-436634	440	10	splicing	splicing	NN
10_1101-436634	440	11	enhancers	enhancer	NNS
10_1101-436634	440	12	in	in	IN
10_1101-436634	440	13	human	human	JJ
10_1101-436634	440	14	genes	gene	NNS
10_1101-436634	440	15	.	.	.
10_1101-436634	441	1	Science	science	NN
10_1101-436634	441	2	297	297	CD
10_1101-436634	441	3	,	,	,
10_1101-436634	441	4	1007–1013	1007–1013	CD
10_1101-436634	441	5	(	(	-LRB-
10_1101-436634	441	6	2002	2002	CD
10_1101-436634	441	7	)	)	-RRB-
10_1101-436634	441	8	.	.	.
10_1101-436634	442	1	12	12	CD
10_1101-436634	442	2	.	.	.
10_1101-436634	443	1	Wang	Wang	NNP
10_1101-436634	443	2	,	,	,
10_1101-436634	443	3	Z.	Z.	NNP
10_1101-436634	443	4	et	et	FW
10_1101-436634	443	5	al	al	NNP
10_1101-436634	443	6	.	.	.
10_1101-436634	444	1	Systematic	systematic	JJ
10_1101-436634	444	2	identification	identification	NN
10_1101-436634	444	3	and	and	CC
10_1101-436634	444	4	analysis	analysis	NN
10_1101-436634	444	5	of	of	IN
10_1101-436634	444	6	exonic	exonic	JJ
10_1101-436634	444	7	splicing	splicing	NN
10_1101-436634	444	8	silencers	silencer	NNS
10_1101-436634	444	9	.	.	.
10_1101-436634	445	1	Cell	cell	NN
10_1101-436634	445	2	119	119	CD
10_1101-436634	445	3	,	,	,
10_1101-436634	445	4	831–845	831–845	CD
10_1101-436634	445	5	(	(	-LRB-
10_1101-436634	445	6	2004	2004	CD
10_1101-436634	445	7	)	)	-RRB-
10_1101-436634	445	8	.	.	.
10_1101-436634	446	1	13	13	CD
10_1101-436634	446	2	.	.	.
10_1101-436634	447	1	Jaganathan	Jaganathan	NNP
10_1101-436634	447	2	,	,	,
10_1101-436634	447	3	K.	K.	NNP
10_1101-436634	447	4	et	et	NNP
10_1101-436634	447	5	al	al	NNP
10_1101-436634	447	6	.	.	.
10_1101-436634	448	1	Predicting	predict	VBG
10_1101-436634	448	2	Splicing	splicing	NN
10_1101-436634	448	3	from	from	IN
10_1101-436634	448	4	Primary	primary	JJ
10_1101-436634	448	5	Sequence	sequence	NN
10_1101-436634	448	6	with	with	IN
10_1101-436634	448	7	Deep	Deep	NNP
10_1101-436634	448	8	Learning	Learning	NNP
10_1101-436634	448	9	.	.	.
10_1101-436634	449	1	Cell	cell	NN
10_1101-436634	449	2	176	176	CD
10_1101-436634	449	3	,	,	,
10_1101-436634	449	4	535–548.e24	535–548.e24	CD
10_1101-436634	449	5	(	(	-LRB-
10_1101-436634	449	6	2019	2019	CD
10_1101-436634	449	7	)	)	-RRB-
10_1101-436634	449	8	.	.	.
10_1101-436634	450	1	14	14	CD
10_1101-436634	450	2	.	.	.
10_1101-436634	451	1	Kahles	Kahles	NNP
10_1101-436634	451	2	,	,	,
10_1101-436634	451	3	A.	a.	NN
10_1101-436634	451	4	,	,	,
10_1101-436634	451	5	Ong	Ong	NNP
10_1101-436634	451	6	,	,	,
10_1101-436634	451	7	C.	C.	NNP
10_1101-436634	451	8	S.	S.	NNP
10_1101-436634	451	9	,	,	,
10_1101-436634	451	10	Zhong	Zhong	NNP
10_1101-436634	451	11	,	,	,
10_1101-436634	451	12	Y.	Y.	NNP
10_1101-436634	452	1	&	&	CC
10_1101-436634	452	2	Rätsch	Rätsch	NNP
10_1101-436634	452	3	,	,	,
10_1101-436634	452	4	G.	G.	NNP
10_1101-436634	452	5	SplAdder	SplAdder	NNP
10_1101-436634	452	6	:	:	:
10_1101-436634	452	7	identification	identification	NN
10_1101-436634	452	8	,	,	,
10_1101-436634	452	9	quantification	quantification	NN
10_1101-436634	452	10	and	and	CC
10_1101-436634	452	11	testing	testing	NN
10_1101-436634	452	12	of	of	IN
10_1101-436634	452	13	alternative	alternative	JJ
10_1101-436634	452	14	splicing	splicing	NN
10_1101-436634	452	15	events	event	NNS
10_1101-436634	452	16	from	from	IN
10_1101-436634	452	17	RNA	RNA	NNP
10_1101-436634	452	18	-	-	HYPH
10_1101-436634	452	19	Seq	Seq	NNP
10_1101-436634	452	20	data	datum	NNS
10_1101-436634	452	21	.	.	.
10_1101-436634	453	1	Bioinformatics	Bioinformatics	NNP
10_1101-436634	453	2	32	32	CD
10_1101-436634	453	3	,	,	,
10_1101-436634	453	4	1840–1847	1840–1847	CD
10_1101-436634	453	5	(	(	-LRB-
10_1101-436634	453	6	2016	2016	CD
10_1101-436634	453	7	)	)	-RRB-
10_1101-436634	453	8	.	.	.
10_1101-436634	454	1	15	15	CD
10_1101-436634	454	2	.	.	.
10_1101-436634	455	1	Trincado	Trincado	NNP
10_1101-436634	455	2	,	,	,
10_1101-436634	455	3	J.	J.	NNP
10_1101-436634	455	4	L.	L.	NNP
10_1101-436634	455	5	et	et	NNP
10_1101-436634	455	6	al	al	NNP
10_1101-436634	455	7	.	.	.
10_1101-436634	456	1	SUPPA2	SUPPA2	NNP
10_1101-436634	456	2	:	:	:
10_1101-436634	456	3	fast	fast	RB
10_1101-436634	456	4	,	,	,
10_1101-436634	456	5	accurate	accurate	JJ
10_1101-436634	456	6	,	,	,
10_1101-436634	456	7	and	and	CC
10_1101-436634	456	8	uncertainty	uncertainty	NN
10_1101-436634	456	9	-	-	HYPH
10_1101-436634	456	10	aware	aware	JJ
10_1101-436634	456	11	differential	differential	NN
10_1101-436634	456	12	splicing	splice	VBG
10_1101-436634	456	13	analysis	analysis	NN
10_1101-436634	456	14	across	across	IN
10_1101-436634	456	15	multiple	multiple	JJ
10_1101-436634	456	16	conditions	condition	NNS
10_1101-436634	456	17	.	.	.
10_1101-436634	457	1	Genome	Genome	NNP
10_1101-436634	457	2	Biol	Biol	NNP
10_1101-436634	457	3	.	.	.
10_1101-436634	458	1	19	19	CD
10_1101-436634	458	2	,	,	,
10_1101-436634	458	3	40	40	CD
10_1101-436634	458	4	(	(	-LRB-
10_1101-436634	458	5	2018	2018	CD
10_1101-436634	458	6	)	)	-RRB-
10_1101-436634	458	7	.	.	.
10_1101-436634	459	1	16	16	CD
10_1101-436634	459	2	.	.	.
10_1101-436634	460	1	Kahles	Kahles	NNP
10_1101-436634	460	2	,	,	,
10_1101-436634	460	3	A.	A.	NNP
10_1101-436634	460	4	et	et	FW
10_1101-436634	460	5	al	al	NNP
10_1101-436634	460	6	.	.	.
10_1101-436634	461	1	Comprehensive	comprehensive	JJ
10_1101-436634	461	2	Analysis	analysis	NN
10_1101-436634	461	3	of	of	IN
10_1101-436634	461	4	Alternative	Alternative	NNP
10_1101-436634	461	5	Splicing	Splicing	NNP
10_1101-436634	461	6	Across	Across	NNP
10_1101-436634	461	7	Tumors	Tumors	NNPS
10_1101-436634	461	8	from	from	IN
10_1101-436634	461	9	8,705	8,705	CD
10_1101-436634	461	10	Patients	patient	NNS
10_1101-436634	461	11	.	.	.
10_1101-436634	462	1	Cancer	Cancer	NNP
10_1101-436634	462	2	Cell	Cell	NNP
10_1101-436634	462	3	34	34	CD
10_1101-436634	462	4	,	,	,
10_1101-436634	462	5	211–224.e6	211–224.e6	CD
10_1101-436634	462	6	(	(	-LRB-
10_1101-436634	462	7	2018	2018	CD
10_1101-436634	462	8	)	)	-RRB-
10_1101-436634	462	9	.	.	.
10_1101-436634	463	1	17	17	CD
10_1101-436634	463	2	.	.	.
10_1101-436634	464	1	Li	Li	NNP
10_1101-436634	464	2	,	,	,
10_1101-436634	464	3	Y.	Y.	NNP
10_1101-436634	464	4	I.	I.	NNP
10_1101-436634	464	5	et	et	NNP
10_1101-436634	464	6	al	al	NNP
10_1101-436634	464	7	.	.	.
10_1101-436634	465	1	Annotation	annotation	NN
10_1101-436634	465	2	-	-	HYPH
10_1101-436634	465	3	free	free	JJ
10_1101-436634	465	4	quantification	quantification	NN
10_1101-436634	465	5	of	of	IN
10_1101-436634	465	6	RNA	RNA	NNP
10_1101-436634	465	7	splicing	splicing	NN
10_1101-436634	465	8	using	use	VBG
10_1101-436634	465	9	LeafCutter	LeafCutter	NNP
10_1101-436634	465	10	.	.	.
10_1101-436634	466	1	Nat	Nat	NNP
10_1101-436634	466	2	.	.	.
10_1101-436634	467	1	Genet	Genet	NNP
10_1101-436634	467	2	.	.	.
10_1101-436634	468	1	50	50	CD
10_1101-436634	468	2	,	,	,
10_1101-436634	468	3	151–158	151–158	CD
10_1101-436634	468	4	(	(	-LRB-
10_1101-436634	468	5	2018	2018	CD
10_1101-436634	468	6	)	)	-RRB-
10_1101-436634	468	7	.	.	.
10_1101-436634	469	1	18	18	CD
10_1101-436634	469	2	.	.	.
10_1101-436634	470	1	Monlong	Monlong	NNP
10_1101-436634	470	2	,	,	,
10_1101-436634	470	3	J.	J.	NNP
10_1101-436634	470	4	,	,	,
10_1101-436634	470	5	Calvo	Calvo	NNP
10_1101-436634	470	6	,	,	,
10_1101-436634	470	7	M.	M.	NNP
10_1101-436634	470	8	,	,	,
10_1101-436634	470	9	Ferreira	Ferreira	NNP
10_1101-436634	470	10	,	,	,
10_1101-436634	470	11	P.	P.	NNP
10_1101-436634	470	12	G.	G.	NNP
10_1101-436634	470	13	&	&	CC
10_1101-436634	470	14	Guigó	Guigó	NNP
10_1101-436634	470	15	,	,	,
10_1101-436634	470	16	R.	R.	NNP
10_1101-436634	470	17	Identification	Identification	NNP
10_1101-436634	470	18	of	of	IN
10_1101-436634	470	19	genetic	genetic	JJ
10_1101-436634	470	20	variants	variant	NNS
10_1101-436634	470	21	associated	associate	VBN
10_1101-436634	470	22	with	with	IN
10_1101-436634	470	23	alternative	alternative	JJ
10_1101-436634	470	24	splicing	splicing	NN
10_1101-436634	470	25	using	use	VBG
10_1101-436634	470	26	sQTLseekeR.	sqtlseeker.	NN
10_1101-436634	471	1	Nat	Nat	NNP
10_1101-436634	471	2	.	.	.
10_1101-436634	472	1	Commun	Commun	VBN
10_1101-436634	472	2	.	.	.
10_1101-436634	473	1	5	5	CD
10_1101-436634	473	2	,	,	,
10_1101-436634	473	3	4698	4698	CD
10_1101-436634	473	4	(	(	-LRB-
10_1101-436634	473	5	2014	2014	CD
10_1101-436634	473	6	)	)	-RRB-
10_1101-436634	473	7	.	.	.
10_1101-436634	474	1	19	19	CD
10_1101-436634	474	2	.	.	.
10_1101-436634	475	1	Li	Li	NNP
10_1101-436634	475	2	,	,	,
10_1101-436634	475	3	Y.	Y.	NNP
10_1101-436634	475	4	I.	I.	NNP
10_1101-436634	475	5	et	et	NNP
10_1101-436634	475	6	al	al	NNP
10_1101-436634	475	7	.	.	.
10_1101-436634	476	1	RNA	RNA	NNP
10_1101-436634	476	2	splicing	splicing	NN
10_1101-436634	476	3	is	be	VBZ
10_1101-436634	476	4	a	a	DT
10_1101-436634	476	5	primary	primary	JJ
10_1101-436634	476	6	link	link	NN
10_1101-436634	476	7	between	between	IN
10_1101-436634	476	8	genetic	genetic	JJ
10_1101-436634	476	9	variation	variation	NN
10_1101-436634	476	10	and	and	CC
10_1101-436634	476	11	disease	disease	NN
10_1101-436634	476	12	.	.	.
10_1101-436634	477	1	Science	science	NN
10_1101-436634	477	2	352	352	CD
10_1101-436634	477	3	,	,	,
10_1101-436634	477	4	600–604	600–604	CD
10_1101-436634	477	5	(	(	-LRB-
10_1101-436634	477	6	2016	2016	CD
10_1101-436634	477	7	)	)	-RRB-
10_1101-436634	477	8	.	.	.
10_1101-436634	478	1	20	20	CD
10_1101-436634	478	2	.	.	.
10_1101-436634	479	1	Jayasinghe	Jayasinghe	NNP
10_1101-436634	479	2	,	,	,
10_1101-436634	479	3	R.	R.	NNP
10_1101-436634	479	4	G.	G.	NNP
10_1101-436634	479	5	et	et	NNP
10_1101-436634	479	6	al	al	NNP
10_1101-436634	479	7	.	.	.
10_1101-436634	480	1	Systematic	systematic	JJ
10_1101-436634	480	2	Analysis	Analysis	NNP
10_1101-436634	480	3	of	of	IN
10_1101-436634	480	4	Splice	Splice	NNP
10_1101-436634	480	5	-	-	HYPH
10_1101-436634	480	6	Site	site	NN
10_1101-436634	480	7	-	-	HYPH
10_1101-436634	480	8	Creating	creating	NN
10_1101-436634	480	9	Mutations	Mutations	NNPS
10_1101-436634	480	10	in	in	IN
10_1101-436634	480	11	Cancer	Cancer	NNP
10_1101-436634	480	12	.	.	.
10_1101-436634	481	1	Cell	Cell	NNP
10_1101-436634	481	2	Rep.	Rep.	NNP
10_1101-436634	481	3	23	23	CD
10_1101-436634	481	4	,	,	,
10_1101-436634	481	5	270–281.e3	270–281.e3	NNS
10_1101-436634	481	6	(	(	-LRB-
10_1101-436634	481	7	2018	2018	CD
10_1101-436634	481	8	)	)	-RRB-
10_1101-436634	481	9	.	.	.
10_1101-436634	482	1	21	21	CD
10_1101-436634	482	2	.	.	.
10_1101-436634	483	1	Viner	Viner	NNP
10_1101-436634	483	2	,	,	,
10_1101-436634	483	3	C.	C.	NNP
10_1101-436634	483	4	,	,	,
10_1101-436634	483	5	Dorman	Dorman	NNP
10_1101-436634	483	6	,	,	,
10_1101-436634	483	7	S.	S.	NNP
10_1101-436634	483	8	N.	N.	NNP
10_1101-436634	483	9	,	,	,
10_1101-436634	483	10	Shirley	Shirley	NNP
10_1101-436634	483	11	,	,	,
10_1101-436634	483	12	B.	B.	NNP
10_1101-436634	483	13	C.	C.	NNP
10_1101-436634	483	14	&	&	CC
10_1101-436634	483	15	Rogan	Rogan	NNP
10_1101-436634	483	16	,	,	,
10_1101-436634	483	17	P.	P.	NNP
10_1101-436634	483	18	K.	K.	NNP
10_1101-436634	483	19	Validation	Validation	NNP
10_1101-436634	483	20	of	of	IN
10_1101-436634	483	21	predicted	predict	VBD
10_1101-436634	483	22	mRNA	mrna	NN
10_1101-436634	483	23	splicing	splicing	NN
10_1101-436634	483	24	mutations	mutation	NNS
10_1101-436634	483	25	using	use	VBG
10_1101-436634	483	26	high	high	JJ
10_1101-436634	483	27	-	-	HYPH
10_1101-436634	483	28	throughput	throughput	NN
10_1101-436634	483	29	transcriptome	transcriptome	DT
10_1101-436634	483	30	data	datum	NNS
10_1101-436634	483	31	.	.	.
10_1101-436634	484	1	F1000Res	f1000re	NNS
10_1101-436634	484	2	.	.	.
10_1101-436634	485	1	3	3	CD
10_1101-436634	485	2	,	,	,
10_1101-436634	485	3	(	(	-LRB-
10_1101-436634	485	4	2014	2014	CD
10_1101-436634	485	5	)	)	-RRB-
10_1101-436634	485	6	.	.	.
10_1101-436634	486	1	22	22	CD
10_1101-436634	486	2	.	.	.
10_1101-436634	487	1	Shirley	Shirley	NNP
10_1101-436634	487	2	,	,	,
10_1101-436634	487	3	B.	B.	NNP
10_1101-436634	487	4	C.	C.	NNP
10_1101-436634	487	5	,	,	,
10_1101-436634	487	6	Mucaki	Mucaki	NNP
10_1101-436634	487	7	,	,	,
10_1101-436634	487	8	E.	E.	NNP
10_1101-436634	487	9	J.	J.	NNP
10_1101-436634	488	1	&	&	CC
10_1101-436634	488	2	Rogan	Rogan	NNP
10_1101-436634	488	3	,	,	,
10_1101-436634	488	4	P.	P.	NNP
10_1101-436634	488	5	K.	K.	NNP
10_1101-436634	488	6	Pan	Pan	NNP
10_1101-436634	488	7	-	-	HYPH
10_1101-436634	488	8	cancer	cancer	NN
10_1101-436634	488	9	repository	repository	NN
10_1101-436634	488	10	of	of	IN
10_1101-436634	488	11	validated	validate	VBN
10_1101-436634	488	12	natural	natural	JJ
10_1101-436634	488	13	and	and	CC
10_1101-436634	488	14	cryptic	cryptic	JJ
10_1101-436634	488	15	mRNA	mrna	NN
10_1101-436634	488	16	splicing	splicing	NN
10_1101-436634	488	17	mutations	mutation	NNS
10_1101-436634	488	18	.	.	.
10_1101-436634	489	1	F1000Res	f1000re	NNS
10_1101-436634	489	2	.	.	.
10_1101-436634	490	1	7	7	CD
10_1101-436634	490	2	,	,	,
10_1101-436634	490	3	1908	1908	CD
10_1101-436634	490	4	(	(	-LRB-
10_1101-436634	490	5	2018	2018	CD
10_1101-436634	490	6	)	)	-RRB-
10_1101-436634	490	7	.	.	.
10_1101-436634	491	1	23	23	CD
10_1101-436634	491	2	.	.	.
10_1101-436634	492	1	Shiraishi	Shiraishi	NNP
10_1101-436634	492	2	,	,	,
10_1101-436634	492	3	Y.	Y.	NNP
10_1101-436634	492	4	et	et	NNP
10_1101-436634	492	5	al	al	NNP
10_1101-436634	492	6	.	.	.
10_1101-436634	493	1	A	a	DT
10_1101-436634	493	2	comprehensive	comprehensive	JJ
10_1101-436634	493	3	characterization	characterization	NN
10_1101-436634	493	4	of	of	IN
10_1101-436634	493	5	cis	cis	NN
10_1101-436634	493	6	-	-	HYPH
10_1101-436634	493	7	acting	act	VBG
10_1101-436634	493	8	splicing	splicing	NN
10_1101-436634	493	9	-	-	HYPH
10_1101-436634	493	10	associated	associate	VBN
10_1101-436634	493	11	.CC	.CC	:
10_1101-436634	493	12	-	-	:
10_1101-436634	493	13	BY	by	IN
10_1101-436634	493	14	-	-	HYPH
10_1101-436634	493	15	NC	NC	NNP
10_1101-436634	493	16	-	-	HYPH
10_1101-436634	493	17	ND	ND	NNP
10_1101-436634	493	18	4.0	4.0	CD
10_1101-436634	493	19	International	international	JJ
10_1101-436634	493	20	licensea	licensea	NNS
10_1101-436634	493	21	certified	certify	VBN
10_1101-436634	493	22	by	by	IN
10_1101-436634	493	23	peer	peer	NN
10_1101-436634	493	24	review	review	NN
10_1101-436634	493	25	)	)	-RRB-
10_1101-436634	493	26	is	be	VBZ
10_1101-436634	493	27	the	the	DT
10_1101-436634	493	28	author	author	NN
10_1101-436634	493	29	/	/	SYM
10_1101-436634	493	30	funder	funder	NN
10_1101-436634	493	31	,	,	,
10_1101-436634	493	32	who	who	WP
10_1101-436634	493	33	has	have	VBZ
10_1101-436634	493	34	granted	grant	VBN
10_1101-436634	493	35	bioRxiv	biorxiv	IN
10_1101-436634	493	36	a	a	DT
10_1101-436634	493	37	license	license	NN
10_1101-436634	493	38	to	to	TO
10_1101-436634	493	39	display	display	VB
10_1101-436634	493	40	the	the	DT
10_1101-436634	493	41	preprint	preprint	NN
10_1101-436634	493	42	in	in	IN
10_1101-436634	493	43	perpetuity	perpetuity	NN
10_1101-436634	493	44	.	.	.
10_1101-436634	494	1	It	-PRON-	PRP
10_1101-436634	494	2	is	be	VBZ
10_1101-436634	494	3	made	make	VBN
10_1101-436634	494	4	available	available	JJ
10_1101-436634	494	5	under	under	IN
10_1101-436634	494	6	The	the	DT
10_1101-436634	494	7	copyright	copyright	NN
10_1101-436634	494	8	holder	holder	NN
10_1101-436634	494	9	for	for	IN
10_1101-436634	494	10	this	this	DT
10_1101-436634	494	11	preprint	preprint	NN
10_1101-436634	494	12	(	(	-LRB-
10_1101-436634	494	13	which	which	WDT
10_1101-436634	494	14	was	be	VBD
10_1101-436634	494	15	notthis	notthis	DT
10_1101-436634	494	16	version	version	NN
10_1101-436634	494	17	posted	post	VBN
10_1101-436634	494	18	January	January	NNP
10_1101-436634	494	19	5	5	CD
10_1101-436634	494	20	,	,	,
10_1101-436634	494	21	2021	2021	CD
10_1101-436634	494	22	.	.	.
10_1101-436634	494	23	;	;	:
10_1101-436634	494	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	494	25	:	:	:
10_1101-436634	494	26	bioRxiv	biorxiv	VB
10_1101-436634	494	27	preprint	preprint	NN
10_1101-436634	494	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	494	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	RB
10_1101-436634	494	30	20	20	CD
10_1101-436634	494	31	variants	variant	NNS
10_1101-436634	494	32	in	in	IN
10_1101-436634	494	33	human	human	JJ
10_1101-436634	494	34	cancer	cancer	NN
10_1101-436634	494	35	.	.	.
10_1101-436634	495	1	Genome	Genome	NNP
10_1101-436634	495	2	Res	Res	NNP
10_1101-436634	495	3	.	.	.
10_1101-436634	496	1	28	28	CD
10_1101-436634	496	2	,	,	,
10_1101-436634	496	3	1111–1125	1111–1125	CD
10_1101-436634	496	4	(	(	-LRB-
10_1101-436634	496	5	2018	2018	CD
10_1101-436634	496	6	)	)	-RRB-
10_1101-436634	496	7	.	.	.
10_1101-436634	497	1	24	24	CD
10_1101-436634	497	2	.	.	.
10_1101-436634	498	1	GTEx	GTEx	VBZ
10_1101-436634	498	2	Consortium	Consortium	NNP
10_1101-436634	498	3	.	.	.
10_1101-436634	499	1	The	the	DT
10_1101-436634	499	2	Genotype	Genotype	NNP
10_1101-436634	499	3	-	-	HYPH
10_1101-436634	499	4	Tissue	Tissue	NNP
10_1101-436634	499	5	Expression	expression	NN
10_1101-436634	499	6	(	(	-LRB-
10_1101-436634	499	7	GTEx	GTEx	NNP
10_1101-436634	499	8	)	)	-RRB-
10_1101-436634	499	9	project	project	NN
10_1101-436634	499	10	.	.	.
10_1101-436634	500	1	Nat	Nat	NNP
10_1101-436634	500	2	.	.	.
10_1101-436634	501	1	Genet	Genet	NNP
10_1101-436634	501	2	.	.	.
10_1101-436634	502	1	45	45	CD
10_1101-436634	502	2	,	,	,
10_1101-436634	502	3	580	580	CD
10_1101-436634	502	4	–	–	:
10_1101-436634	502	5	585	585	CD
10_1101-436634	502	6	(	(	-LRB-
10_1101-436634	502	7	2013	2013	CD
10_1101-436634	502	8	)	)	-RRB-
10_1101-436634	502	9	.	.	.
10_1101-436634	503	1	25	25	CD
10_1101-436634	503	2	.	.	.
10_1101-436634	504	1	McLaren	McLaren	NNP
10_1101-436634	504	2	,	,	,
10_1101-436634	504	3	W.	W.	NNP
10_1101-436634	504	4	et	et	NNP
10_1101-436634	504	5	al	al	NNP
10_1101-436634	504	6	.	.	.
10_1101-436634	505	1	The	the	DT
10_1101-436634	505	2	Ensembl	Ensembl	NNP
10_1101-436634	505	3	Variant	Variant	NNP
10_1101-436634	505	4	Effect	Effect	NNP
10_1101-436634	505	5	Predictor	Predictor	NNP
10_1101-436634	505	6	.	.	.
10_1101-436634	506	1	Genome	Genome	NNP
10_1101-436634	506	2	Biol	Biol	NNP
10_1101-436634	506	3	.	.	.
10_1101-436634	507	1	17	17	CD
10_1101-436634	507	2	,	,	,
10_1101-436634	507	3	122	122	CD
10_1101-436634	507	4	(	(	-LRB-
10_1101-436634	507	5	2016	2016	CD
10_1101-436634	507	6	)	)	-RRB-
10_1101-436634	507	7	.	.	.
10_1101-436634	508	1	26	26	CD
10_1101-436634	508	2	.	.	.
10_1101-436634	509	1	Li	Li	NNP
10_1101-436634	509	2	,	,	,
10_1101-436634	509	3	H.	H.	NNP
10_1101-436634	509	4	et	et	NNP
10_1101-436634	509	5	al	al	NNP
10_1101-436634	509	6	.	.	.
10_1101-436634	510	1	The	the	DT
10_1101-436634	510	2	Sequence	Sequence	NNP
10_1101-436634	510	3	Alignment	Alignment	NNP
10_1101-436634	510	4	/	/	SYM
10_1101-436634	510	5	Map	Map	NNP
10_1101-436634	510	6	format	format	NN
10_1101-436634	510	7	and	and	CC
10_1101-436634	510	8	SAMtools	samtool	NNS
10_1101-436634	510	9	.	.	.
10_1101-436634	511	1	Bioinformatics	Bioinformatics	NNP
10_1101-436634	511	2	25	25	CD
10_1101-436634	511	3	,	,	,
10_1101-436634	511	4	2078	2078	CD
10_1101-436634	511	5	–	–	:
10_1101-436634	511	6	2079	2079	CD
10_1101-436634	511	7	(	(	-LRB-
10_1101-436634	511	8	2009	2009	CD
10_1101-436634	511	9	)	)	-RRB-
10_1101-436634	511	10	.	.	.
10_1101-436634	512	1	27	27	CD
10_1101-436634	512	2	.	.	.
10_1101-436634	513	1	Sondka	sondka	NN
10_1101-436634	513	2	,	,	,
10_1101-436634	513	3	Z.	Z.	NNP
10_1101-436634	513	4	et	et	FW
10_1101-436634	513	5	al	al	NNP
10_1101-436634	513	6	.	.	.
10_1101-436634	514	1	The	the	DT
10_1101-436634	514	2	COSMIC	COSMIC	NNP
10_1101-436634	514	3	Cancer	Cancer	NNP
10_1101-436634	514	4	Gene	Gene	NNP
10_1101-436634	514	5	Census	Census	NNP
10_1101-436634	514	6	:	:	:
10_1101-436634	514	7	describing	describe	VBG
10_1101-436634	514	8	genetic	genetic	JJ
10_1101-436634	514	9	dysfunction	dysfunction	NN
10_1101-436634	514	10	across	across	IN
10_1101-436634	514	11	all	all	DT
10_1101-436634	514	12	human	human	JJ
10_1101-436634	514	13	cancers	cancer	NNS
10_1101-436634	514	14	.	.	.
10_1101-436634	515	1	Nat	Nat	NNP
10_1101-436634	515	2	.	.	.
10_1101-436634	516	1	Rev.	Rev.	NNP
10_1101-436634	517	1	Cancer	cancer	NN
10_1101-436634	517	2	18	18	CD
10_1101-436634	517	3	,	,	,
10_1101-436634	517	4	696–705	696–705	CD
10_1101-436634	517	5	(	(	-LRB-
10_1101-436634	517	6	2018	2018	CD
10_1101-436634	517	7	)	)	-RRB-
10_1101-436634	517	8	.	.	.
10_1101-436634	518	1	28	28	CD
10_1101-436634	518	2	.	.	.
10_1101-436634	519	1	Robinson	Robinson	NNP
10_1101-436634	519	2	,	,	,
10_1101-436634	519	3	J.	J.	NNP
10_1101-436634	519	4	T.	T.	NNP
10_1101-436634	519	5	et	et	NNP
10_1101-436634	519	6	al	al	NNP
10_1101-436634	519	7	.	.	.
10_1101-436634	520	1	Integrative	integrative	JJ
10_1101-436634	520	2	genomics	genomic	NNS
10_1101-436634	520	3	viewer	viewer	NN
10_1101-436634	520	4	.	.	.
10_1101-436634	521	1	Nat	Nat	NNP
10_1101-436634	521	2	.	.	.
10_1101-436634	522	1	Biotechnol	Biotechnol	NNS
10_1101-436634	522	2	.	.	.
10_1101-436634	523	1	29	29	CD
10_1101-436634	523	2	,	,	,
10_1101-436634	523	3	24–26	24–26	CD
10_1101-436634	523	4	(	(	-LRB-
10_1101-436634	523	5	2011	2011	CD
10_1101-436634	523	6	)	)	-RRB-
10_1101-436634	523	7	.	.	.
10_1101-436634	524	1	29	29	CD
10_1101-436634	524	2	.	.	.
10_1101-436634	525	1	Dobin	Dobin	NNP
10_1101-436634	525	2	,	,	,
10_1101-436634	525	3	A.	A.	NNP
10_1101-436634	525	4	et	et	FW
10_1101-436634	525	5	al	al	NNP
10_1101-436634	525	6	.	.	.
10_1101-436634	526	1	STAR	STAR	NNP
10_1101-436634	526	2	:	:	:
10_1101-436634	526	3	ultrafast	ultrafast	NNP
10_1101-436634	526	4	universal	universal	JJ
10_1101-436634	526	5	RNA	RNA	NNP
10_1101-436634	526	6	-	-	HYPH
10_1101-436634	526	7	seq	seq	NN
10_1101-436634	526	8	aligner	aligner	NN
10_1101-436634	526	9	.	.	.
10_1101-436634	527	1	Bioinformatics	Bioinformatics	NNP
10_1101-436634	527	2	29	29	CD
10_1101-436634	527	3	,	,	,
10_1101-436634	527	4	15–21	15–21	NNP
10_1101-436634	527	5	(	(	-LRB-
10_1101-436634	527	6	2013	2013	CD
10_1101-436634	527	7	)	)	-RRB-
10_1101-436634	527	8	.	.	.
10_1101-436634	528	1	30	30	CD
10_1101-436634	528	2	.	.	.
10_1101-436634	529	1	Kim	Kim	NNP
10_1101-436634	529	2	,	,	,
10_1101-436634	529	3	D.	D.	NNP
10_1101-436634	529	4	,	,	,
10_1101-436634	529	5	Langmead	Langmead	NNP
10_1101-436634	529	6	,	,	,
10_1101-436634	529	7	B.	B.	NNP
10_1101-436634	530	1	&	&	CC
10_1101-436634	530	2	Salzberg	Salzberg	NNP
10_1101-436634	530	3	,	,	,
10_1101-436634	530	4	S.	S.	NNP
10_1101-436634	530	5	L.	L.	NNP
10_1101-436634	530	6	HISAT	HISAT	NNP
10_1101-436634	530	7	:	:	:
10_1101-436634	530	8	a	a	DT
10_1101-436634	530	9	fast	fast	JJ
10_1101-436634	530	10	spliced	spliced	JJ
10_1101-436634	530	11	aligner	aligner	NN
10_1101-436634	530	12	with	with	IN
10_1101-436634	530	13	low	low	JJ
10_1101-436634	530	14	memory	memory	NN
10_1101-436634	530	15	requirements	requirement	NNS
10_1101-436634	530	16	.	.	.
10_1101-436634	531	1	Nat	Nat	NNP
10_1101-436634	531	2	.	.	.
10_1101-436634	532	1	Methods	method	NNS
10_1101-436634	532	2	12	12	CD
10_1101-436634	532	3	,	,	,
10_1101-436634	532	4	357–360	357–360	CD
10_1101-436634	532	5	(	(	-LRB-
10_1101-436634	532	6	2015	2015	CD
10_1101-436634	532	7	)	)	-RRB-
10_1101-436634	532	8	.	.	.
10_1101-436634	533	1	31	31	CD
10_1101-436634	533	2	.	.	.
10_1101-436634	534	1	Kim	Kim	NNP
10_1101-436634	534	2	,	,	,
10_1101-436634	534	3	D.	D.	NNP
10_1101-436634	534	4	et	et	NNP
10_1101-436634	534	5	al	al	NNP
10_1101-436634	534	6	.	.	.
10_1101-436634	535	1	TopHat2	TopHat2	NNP
10_1101-436634	535	2	:	:	:
10_1101-436634	535	3	accurate	accurate	JJ
10_1101-436634	535	4	alignment	alignment	NN
10_1101-436634	535	5	of	of	IN
10_1101-436634	535	6	transcriptomes	transcriptome	NNS
10_1101-436634	535	7	in	in	IN
10_1101-436634	535	8	the	the	DT
10_1101-436634	535	9	presence	presence	NN
10_1101-436634	535	10	of	of	IN
10_1101-436634	535	11	insertions	insertion	NNS
10_1101-436634	535	12	,	,	,
10_1101-436634	535	13	deletions	deletion	NNS
10_1101-436634	535	14	and	and	CC
10_1101-436634	535	15	gene	gene	NN
10_1101-436634	535	16	fusions	fusion	NNS
10_1101-436634	535	17	.	.	.
10_1101-436634	536	1	Genome	Genome	NNP
10_1101-436634	536	2	Biol	Biol	NNP
10_1101-436634	536	3	.	.	.
10_1101-436634	537	1	14	14	CD
10_1101-436634	537	2	,	,	,
10_1101-436634	537	3	R36	R36	NNP
10_1101-436634	537	4	(	(	-LRB-
10_1101-436634	537	5	2013	2013	CD
10_1101-436634	537	6	)	)	-RRB-
10_1101-436634	537	7	.	.	.
10_1101-436634	538	1	32	32	CD
10_1101-436634	538	2	.	.	.
10_1101-436634	539	1	Conway	Conway	NNP
10_1101-436634	539	2	,	,	,
10_1101-436634	539	3	J.	J.	NNP
10_1101-436634	539	4	R.	R.	NNP
10_1101-436634	539	5	,	,	,
10_1101-436634	539	6	Lex	Lex	NNP
10_1101-436634	539	7	,	,	,
10_1101-436634	539	8	A.	a.	NN
10_1101-436634	540	1	&	&	CC
10_1101-436634	540	2	Gehlenborg	Gehlenborg	NNP
10_1101-436634	540	3	,	,	,
10_1101-436634	540	4	N.	N.	NNP
10_1101-436634	540	5	UpSetR	UpSetR	NNP
10_1101-436634	540	6	:	:	:
10_1101-436634	540	7	an	an	DT
10_1101-436634	540	8	R	r	NN
10_1101-436634	540	9	package	package	NN
10_1101-436634	540	10	for	for	IN
10_1101-436634	540	11	the	the	DT
10_1101-436634	540	12	visualization	visualization	NN
10_1101-436634	540	13	of	of	IN
10_1101-436634	540	14	intersecting	intersect	VBG
10_1101-436634	540	15	sets	set	NNS
10_1101-436634	540	16	and	and	CC
10_1101-436634	540	17	their	-PRON-	PRP$
10_1101-436634	540	18	properties	property	NNS
10_1101-436634	540	19	.	.	.
10_1101-436634	541	1	Bioinformatics	Bioinformatics	NNP
10_1101-436634	541	2	33	33	CD
10_1101-436634	541	3	,	,	,
10_1101-436634	541	4	2938–2940	2938–2940	CD
10_1101-436634	541	5	(	(	-LRB-
10_1101-436634	541	6	2017	2017	CD
10_1101-436634	541	7	)	)	-RRB-
10_1101-436634	541	8	.	.	.
10_1101-436634	542	1	33	33	CD
10_1101-436634	542	2	.	.	.
10_1101-436634	543	1	Surget	Surget	NNP
10_1101-436634	543	2	,	,	,
10_1101-436634	543	3	S.	S.	NNP
10_1101-436634	543	4	,	,	,
10_1101-436634	543	5	Khoury	Khoury	NNP
10_1101-436634	543	6	,	,	,
10_1101-436634	543	7	M.	M.	NNP
10_1101-436634	543	8	P.	P.	NNP
10_1101-436634	543	9	&	&	CC
10_1101-436634	543	10	Bourdon	Bourdon	NNP
10_1101-436634	543	11	,	,	,
10_1101-436634	543	12	J.-C.	J.-C.	NNP
10_1101-436634	543	13	Uncovering	uncover	VBG
10_1101-436634	543	14	the	the	DT
10_1101-436634	543	15	role	role	NN
10_1101-436634	543	16	of	of	IN
10_1101-436634	543	17	p53	p53	NN
10_1101-436634	543	18	splice	splice	NN
10_1101-436634	543	19	variants	variant	NNS
10_1101-436634	543	20	in	in	IN
10_1101-436634	543	21	human	human	JJ
10_1101-436634	543	22	malignancy	malignancy	NN
10_1101-436634	543	23	:	:	:
10_1101-436634	543	24	a	a	DT
10_1101-436634	543	25	clinical	clinical	JJ
10_1101-436634	543	26	perspective	perspective	NN
10_1101-436634	543	27	.	.	.
10_1101-436634	544	1	Onco	Onco	NNP
10_1101-436634	544	2	.	.	.
10_1101-436634	545	1	Targets	target	NNS
10_1101-436634	545	2	.	.	.
10_1101-436634	546	1	Ther	ther	RB
10_1101-436634	546	2	.	.	.
10_1101-436634	547	1	7	7	CD
10_1101-436634	547	2	,	,	,
10_1101-436634	547	3	57–68	57–68	CD
10_1101-436634	547	4	(	(	-LRB-
10_1101-436634	547	5	2013	2013	CD
10_1101-436634	547	6	)	)	-RRB-
10_1101-436634	547	7	.	.	.
10_1101-436634	548	1	34	34	CD
10_1101-436634	548	2	.	.	.
10_1101-436634	549	1	Tokheim	Tokheim	NNP
10_1101-436634	549	2	,	,	,
10_1101-436634	549	3	C.	C.	NNP
10_1101-436634	549	4	&	&	CC
10_1101-436634	549	5	Karchin	Karchin	NNP
10_1101-436634	549	6	,	,	,
10_1101-436634	549	7	R.	R.	NNP
10_1101-436634	549	8	CHASMplus	CHASMplus	NNP
10_1101-436634	549	9	Reveals	reveal	VBZ
10_1101-436634	549	10	the	the	DT
10_1101-436634	549	11	Scope	Scope	NNP
10_1101-436634	549	12	of	of	IN
10_1101-436634	549	13	Somatic	Somatic	NNP
10_1101-436634	549	14	Missense	Missense	NNP
10_1101-436634	549	15	Mutations	mutation	NNS
10_1101-436634	549	16	Driving	Driving	NNP
10_1101-436634	549	17	Human	Human	NNP
10_1101-436634	549	18	Cancers	Cancers	NNPS
10_1101-436634	549	19	.	.	.
10_1101-436634	550	1	Cell	Cell	NNP
10_1101-436634	550	2	Syst	Syst	NNP
10_1101-436634	550	3	9	9	CD
10_1101-436634	550	4	,	,	,
10_1101-436634	550	5	9–23.e8	9–23.e8	CD
10_1101-436634	550	6	(	(	-LRB-
10_1101-436634	550	7	2019	2019	CD
10_1101-436634	550	8	)	)	-RRB-
10_1101-436634	550	9	.	.	.
10_1101-436634	551	1	35	35	CD
10_1101-436634	551	2	.	.	.
10_1101-436634	552	1	Bicknell	Bicknell	NNP
10_1101-436634	552	2	,	,	,
10_1101-436634	552	3	D.	D.	NNP
10_1101-436634	552	4	C.	C.	NNP
10_1101-436634	552	5	,	,	,
10_1101-436634	552	6	Kaklamanis	Kaklamanis	NNP
10_1101-436634	552	7	,	,	,
10_1101-436634	552	8	L.	L.	NNP
10_1101-436634	552	9	,	,	,
10_1101-436634	552	10	Hampson	Hampson	NNP
10_1101-436634	552	11	,	,	,
10_1101-436634	552	12	R.	R.	NNP
10_1101-436634	552	13	,	,	,
10_1101-436634	552	14	Bodmer	Bodmer	NNP
10_1101-436634	552	15	,	,	,
10_1101-436634	552	16	W.	W.	NNP
10_1101-436634	552	17	F.	F.	NNP
10_1101-436634	552	18	&	&	CC
10_1101-436634	552	19	Karran	Karran	NNP
10_1101-436634	552	20	,	,	,
10_1101-436634	552	21	P.	P.	NNP
10_1101-436634	552	22	Selection	Selection	NNP
10_1101-436634	552	23	for	for	IN
10_1101-436634	552	24	β2-	β2-	NNP
10_1101-436634	552	25	microglobulin	microglobulin	NNP
10_1101-436634	552	26	mutation	mutation	NN
10_1101-436634	552	27	in	in	IN
10_1101-436634	552	28	mismatch	mismatch	NN
10_1101-436634	552	29	repair	repair	NN
10_1101-436634	552	30	-	-	HYPH
10_1101-436634	552	31	defective	defective	JJ
10_1101-436634	552	32	colorectal	colorectal	JJ
10_1101-436634	552	33	carcinomas	carcinoma	NNS
10_1101-436634	552	34	.	.	.
10_1101-436634	553	1	Curr	curr	UH
10_1101-436634	553	2	.	.	.
10_1101-436634	554	1	Biol	Biol	NNP
10_1101-436634	554	2	.	.	.
10_1101-436634	555	1	6	6	CD
10_1101-436634	555	2	,	,	,
10_1101-436634	555	3	1695–1697	1695–1697	CD
10_1101-436634	555	4	(	(	-LRB-
10_1101-436634	555	5	1996	1996	CD
10_1101-436634	555	6	)	)	-RRB-
10_1101-436634	555	7	.	.	.
10_1101-436634	556	1	36	36	CD
10_1101-436634	556	2	.	.	.
10_1101-436634	557	1	Bonneville	Bonneville	NNP
10_1101-436634	557	2	,	,	,
10_1101-436634	557	3	R.	R.	NNP
10_1101-436634	557	4	et	et	NNP
10_1101-436634	557	5	al	al	NNP
10_1101-436634	557	6	.	.	.
10_1101-436634	558	1	Landscape	Landscape	NNP
10_1101-436634	558	2	of	of	IN
10_1101-436634	558	3	Microsatellite	Microsatellite	NNP
10_1101-436634	558	4	Instability	Instability	NNP
10_1101-436634	558	5	Across	Across	NNP
10_1101-436634	558	6	39	39	CD
10_1101-436634	558	7	Cancer	Cancer	NNP
10_1101-436634	558	8	Types	Types	NNPS
10_1101-436634	558	9	.	.	.
10_1101-436634	559	1	JCO	JCO	NNP
10_1101-436634	559	2	Precis	Precis	NNP
10_1101-436634	559	3	Oncol	Oncol	NNP
10_1101-436634	559	4	2017	2017	CD
10_1101-436634	559	5	,	,	,
10_1101-436634	559	6	(	(	-LRB-
10_1101-436634	559	7	2017	2017	CD
10_1101-436634	559	8	)	)	-RRB-
10_1101-436634	559	9	.	.	.
10_1101-436634	560	1	37	37	CD
10_1101-436634	560	2	.	.	.
10_1101-436634	561	1	Kloor	Kloor	NNP
10_1101-436634	561	2	,	,	,
10_1101-436634	561	3	M.	M.	NNP
10_1101-436634	561	4	et	et	NNP
10_1101-436634	561	5	al	al	NNP
10_1101-436634	561	6	.	.	.
10_1101-436634	562	1	Immunoselective	immunoselective	JJ
10_1101-436634	562	2	pressure	pressure	NN
10_1101-436634	562	3	and	and	CC
10_1101-436634	562	4	human	human	JJ
10_1101-436634	562	5	leukocyte	leukocyte	NN
10_1101-436634	562	6	antigen	antigen	NNP
10_1101-436634	562	7	class	class	NNP
10_1101-436634	562	8	I	-PRON-	PRP
10_1101-436634	562	9	antigen	antigen	VBP
10_1101-436634	562	10	.CC	.CC	NFP
10_1101-436634	562	11	-	-	:
10_1101-436634	562	12	BY	by	IN
10_1101-436634	562	13	-	-	HYPH
10_1101-436634	562	14	NC	NC	NNP
10_1101-436634	562	15	-	-	HYPH
10_1101-436634	562	16	ND	ND	NNP
10_1101-436634	562	17	4.0	4.0	CD
10_1101-436634	562	18	International	international	JJ
10_1101-436634	562	19	licensea	licensea	NNS
10_1101-436634	562	20	certified	certify	VBN
10_1101-436634	562	21	by	by	IN
10_1101-436634	562	22	peer	peer	NN
10_1101-436634	562	23	review	review	NN
10_1101-436634	562	24	)	)	-RRB-
10_1101-436634	562	25	is	be	VBZ
10_1101-436634	562	26	the	the	DT
10_1101-436634	562	27	author	author	NN
10_1101-436634	562	28	/	/	SYM
10_1101-436634	562	29	funder	funder	NN
10_1101-436634	562	30	,	,	,
10_1101-436634	562	31	who	who	WP
10_1101-436634	562	32	has	have	VBZ
10_1101-436634	562	33	granted	grant	VBN
10_1101-436634	562	34	bioRxiv	biorxiv	IN
10_1101-436634	562	35	a	a	DT
10_1101-436634	562	36	license	license	NN
10_1101-436634	562	37	to	to	TO
10_1101-436634	562	38	display	display	VB
10_1101-436634	562	39	the	the	DT
10_1101-436634	562	40	preprint	preprint	NN
10_1101-436634	562	41	in	in	IN
10_1101-436634	562	42	perpetuity	perpetuity	NN
10_1101-436634	562	43	.	.	.
10_1101-436634	563	1	It	-PRON-	PRP
10_1101-436634	563	2	is	be	VBZ
10_1101-436634	563	3	made	make	VBN
10_1101-436634	563	4	available	available	JJ
10_1101-436634	563	5	under	under	IN
10_1101-436634	563	6	The	the	DT
10_1101-436634	563	7	copyright	copyright	NN
10_1101-436634	563	8	holder	holder	NN
10_1101-436634	563	9	for	for	IN
10_1101-436634	563	10	this	this	DT
10_1101-436634	563	11	preprint	preprint	NN
10_1101-436634	563	12	(	(	-LRB-
10_1101-436634	563	13	which	which	WDT
10_1101-436634	563	14	was	be	VBD
10_1101-436634	563	15	notthis	notthis	DT
10_1101-436634	563	16	version	version	NN
10_1101-436634	563	17	posted	post	VBN
10_1101-436634	563	18	January	January	NNP
10_1101-436634	563	19	5	5	CD
10_1101-436634	563	20	,	,	,
10_1101-436634	563	21	2021	2021	CD
10_1101-436634	563	22	.	.	.
10_1101-436634	563	23	;	;	:
10_1101-436634	563	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	563	25	:	:	:
10_1101-436634	563	26	bioRxiv	biorxiv	VB
10_1101-436634	563	27	preprint	preprint	NN
10_1101-436634	563	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	563	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	563	30	21	21	CD
10_1101-436634	563	31	machinery	machinery	NN
10_1101-436634	563	32	defects	defect	NNS
10_1101-436634	563	33	in	in	IN
10_1101-436634	563	34	microsatellite	microsatellite	NNP
10_1101-436634	563	35	unstable	unstable	JJ
10_1101-436634	563	36	colorectal	colorectal	JJ
10_1101-436634	563	37	cancers	cancer	NNS
10_1101-436634	563	38	.	.	.
10_1101-436634	564	1	Cancer	cancer	NN
10_1101-436634	564	2	Res	Res	NNP
10_1101-436634	564	3	.	.	.
10_1101-436634	565	1	65	65	CD
10_1101-436634	565	2	,	,	,
10_1101-436634	565	3	6418	6418	CD
10_1101-436634	565	4	–	–	:
10_1101-436634	565	5	6424	6424	CD
10_1101-436634	565	6	(	(	-LRB-
10_1101-436634	565	7	2005	2005	CD
10_1101-436634	565	8	)	)	-RRB-
10_1101-436634	565	9	.	.	.
10_1101-436634	566	1	38	38	CD
10_1101-436634	566	2	.	.	.
10_1101-436634	567	1	Sade	Sade	NNP
10_1101-436634	567	2	-	-	HYPH
10_1101-436634	567	3	Feldman	Feldman	NNP
10_1101-436634	567	4	,	,	,
10_1101-436634	567	5	M.	M.	NNP
10_1101-436634	567	6	et	et	NNP
10_1101-436634	567	7	al	al	NNP
10_1101-436634	567	8	.	.	.
10_1101-436634	568	1	Resistance	resistance	NN
10_1101-436634	568	2	to	to	TO
10_1101-436634	568	3	checkpoint	checkpoint	VB
10_1101-436634	568	4	blockade	blockade	NN
10_1101-436634	568	5	therapy	therapy	NN
10_1101-436634	568	6	through	through	IN
10_1101-436634	568	7	inactivation	inactivation	NN
10_1101-436634	568	8	of	of	IN
10_1101-436634	568	9	antigen	antigen	NNP
10_1101-436634	568	10	presentation	presentation	NNP
10_1101-436634	568	11	.	.	.
10_1101-436634	569	1	Nat	Nat	NNP
10_1101-436634	569	2	.	.	.
10_1101-436634	570	1	Commun	Commun	VBN
10_1101-436634	570	2	.	.	.
10_1101-436634	571	1	8	8	CD
10_1101-436634	571	2	,	,	,
10_1101-436634	571	3	1136	1136	CD
10_1101-436634	571	4	(	(	-LRB-
10_1101-436634	571	5	2017	2017	CD
10_1101-436634	571	6	)	)	-RRB-
10_1101-436634	571	7	.	.	.
10_1101-436634	572	1	39	39	CD
10_1101-436634	572	2	.	.	.
10_1101-436634	573	1	Seliger	Seliger	NNP
10_1101-436634	573	2	,	,	,
10_1101-436634	573	3	B.	B.	NNP
10_1101-436634	573	4	,	,	,
10_1101-436634	573	5	Maeurer	Maeurer	NNP
10_1101-436634	573	6	,	,	,
10_1101-436634	573	7	M.	M.	NNP
10_1101-436634	573	8	J.	J.	NNP
10_1101-436634	574	1	&	&	CC
10_1101-436634	574	2	Ferrone	Ferrone	NNP
10_1101-436634	574	3	,	,	,
10_1101-436634	574	4	S.	S.	NNP
10_1101-436634	574	5	Antigen	Antigen	NNP
10_1101-436634	574	6	-	-	HYPH
10_1101-436634	574	7	processing	process	VBG
10_1101-436634	574	8	machinery	machinery	NN
10_1101-436634	574	9	breakdown	breakdown	NN
10_1101-436634	574	10	and	and	CC
10_1101-436634	574	11	tumor	tumor	NN
10_1101-436634	574	12	growth	growth	NN
10_1101-436634	574	13	.	.	.
10_1101-436634	575	1	Immunol	immunol	NN
10_1101-436634	575	2	.	.	.
10_1101-436634	576	1	Today	today	NN
10_1101-436634	576	2	21	21	CD
10_1101-436634	576	3	,	,	,
10_1101-436634	576	4	455–464	455–464	CD
10_1101-436634	576	5	(	(	-LRB-
10_1101-436634	576	6	2000	2000	CD
10_1101-436634	576	7	)	)	-RRB-
10_1101-436634	576	8	.	.	.
10_1101-436634	577	1	40	40	CD
10_1101-436634	577	2	.	.	.
10_1101-436634	578	1	Güssow	Güssow	NNP
10_1101-436634	578	2	,	,	,
10_1101-436634	578	3	D.	D.	NNP
10_1101-436634	578	4	et	et	NNP
10_1101-436634	578	5	al	al	NNP
10_1101-436634	578	6	.	.	.
10_1101-436634	579	1	The	the	DT
10_1101-436634	579	2	human	human	JJ
10_1101-436634	579	3	beta	beta	NN
10_1101-436634	579	4	2-microglobulin	2-microglobulin	CD
10_1101-436634	579	5	gene	gene	NN
10_1101-436634	579	6	.	.	.
10_1101-436634	580	1	Primary	primary	JJ
10_1101-436634	580	2	structure	structure	NN
10_1101-436634	580	3	and	and	CC
10_1101-436634	580	4	definition	definition	NN
10_1101-436634	580	5	of	of	IN
10_1101-436634	580	6	the	the	DT
10_1101-436634	580	7	transcriptional	transcriptional	JJ
10_1101-436634	580	8	unit	unit	NN
10_1101-436634	580	9	.	.	.
10_1101-436634	581	1	J.	J.	NNP
10_1101-436634	581	2	Immunol	Immunol	NNP
10_1101-436634	581	3	.	.	.
10_1101-436634	582	1	139	139	CD
10_1101-436634	582	2	,	,	,
10_1101-436634	582	3	3132–3138	3132–3138	CD
10_1101-436634	582	4	(	(	-LRB-
10_1101-436634	582	5	1987	1987	CD
10_1101-436634	582	6	)	)	-RRB-
10_1101-436634	582	7	.	.	.
10_1101-436634	583	1	41	41	CD
10_1101-436634	583	2	.	.	.
10_1101-436634	584	1	Wang	Wang	NNP
10_1101-436634	584	2	,	,	,
10_1101-436634	584	3	L.	L.	NNP
10_1101-436634	584	4	,	,	,
10_1101-436634	584	5	Yin	Yin	NNP
10_1101-436634	584	6	,	,	,
10_1101-436634	584	7	W.	W.	NNP
10_1101-436634	584	8	&	&	CC
10_1101-436634	584	9	Shi	Shi	NNP
10_1101-436634	584	10	,	,	,
10_1101-436634	584	11	C.	C.	NNP
10_1101-436634	584	12	E3	E3	NNP
10_1101-436634	584	13	ubiquitin	ubiquitin	JJ
10_1101-436634	584	14	ligase	ligase	NN
10_1101-436634	584	15	,	,	,
10_1101-436634	584	16	RNF139	RNF139	NNP
10_1101-436634	584	17	,	,	,
10_1101-436634	584	18	inhibits	inhibit	VBZ
10_1101-436634	584	19	the	the	DT
10_1101-436634	584	20	progression	progression	NN
10_1101-436634	584	21	of	of	IN
10_1101-436634	584	22	tongue	tongue	NN
10_1101-436634	584	23	cancer	cancer	NN
10_1101-436634	584	24	.	.	.
10_1101-436634	585	1	BMC	BMC	NNP
10_1101-436634	585	2	Cancer	Cancer	NNP
10_1101-436634	585	3	17	17	CD
10_1101-436634	585	4	,	,	,
10_1101-436634	585	5	452	452	CD
10_1101-436634	585	6	(	(	-LRB-
10_1101-436634	585	7	2017	2017	CD
10_1101-436634	585	8	)	)	-RRB-
10_1101-436634	585	9	.	.	.
10_1101-436634	586	1	42	42	CD
10_1101-436634	586	2	.	.	.
10_1101-436634	587	1	Hornbeck	Hornbeck	NNP
10_1101-436634	587	2	,	,	,
10_1101-436634	587	3	P.	P.	NNP
10_1101-436634	587	4	V.	V.	NNP
10_1101-436634	587	5	et	et	NNP
10_1101-436634	587	6	al	al	NNP
10_1101-436634	587	7	.	.	.
10_1101-436634	588	1	PhosphoSitePlus	PhosphoSitePlus	NNP
10_1101-436634	588	2	,	,	,
10_1101-436634	588	3	2014	2014	CD
10_1101-436634	588	4	:	:	:
10_1101-436634	588	5	mutations	mutation	NNS
10_1101-436634	588	6	,	,	,
10_1101-436634	588	7	PTMs	ptm	NNS
10_1101-436634	588	8	and	and	CC
10_1101-436634	588	9	recalibrations	recalibration	NNS
10_1101-436634	588	10	.	.	.
10_1101-436634	589	1	Nucleic	Nucleic	NNP
10_1101-436634	589	2	Acids	Acids	NNPS
10_1101-436634	589	3	Res	Res	NNP
10_1101-436634	589	4	.	.	.
10_1101-436634	590	1	43	43	CD
10_1101-436634	590	2	,	,	,
10_1101-436634	590	3	D512–20	D512–20	NNP
10_1101-436634	590	4	(	(	-LRB-
10_1101-436634	590	5	2015	2015	CD
10_1101-436634	590	6	)	)	-RRB-
10_1101-436634	590	7	.	.	.
10_1101-436634	591	1	43	43	CD
10_1101-436634	591	2	.	.	.
10_1101-436634	592	1	Zhao	Zhao	NNP
10_1101-436634	592	2	,	,	,
10_1101-436634	592	3	R.	R.	NNP
10_1101-436634	592	4	,	,	,
10_1101-436634	592	5	Choi	Choi	NNP
10_1101-436634	592	6	,	,	,
10_1101-436634	592	7	B.	B.	NNP
10_1101-436634	592	8	Y.	Y.	NNP
10_1101-436634	592	9	,	,	,
10_1101-436634	592	10	Lee	Lee	NNP
10_1101-436634	592	11	,	,	,
10_1101-436634	592	12	M.-H.	M.-H.	NNP
10_1101-436634	592	13	,	,	,
10_1101-436634	592	14	Bode	Bode	NNP
10_1101-436634	592	15	,	,	,
10_1101-436634	592	16	A.	A.	NNP
10_1101-436634	592	17	M.	M.	NNP
10_1101-436634	592	18	&	&	CC
10_1101-436634	592	19	Dong	Dong	NNP
10_1101-436634	592	20	,	,	,
10_1101-436634	592	21	Z.	Z.	NNP
10_1101-436634	593	1	Implications	implication	NNS
10_1101-436634	593	2	of	of	IN
10_1101-436634	593	3	Genetic	Genetic	NNP
10_1101-436634	593	4	and	and	CC
10_1101-436634	593	5	Epigenetic	Epigenetic	NNP
10_1101-436634	593	6	Alterations	Alterations	NNPS
10_1101-436634	593	7	of	of	IN
10_1101-436634	593	8	CDKN2A	CDKN2A	NNP
10_1101-436634	593	9	(	(	-LRB-
10_1101-436634	593	10	p16(INK4a	p16(INK4a	NNP
10_1101-436634	593	11	)	)	-RRB-
10_1101-436634	593	12	)	)	-RRB-
10_1101-436634	593	13	in	in	IN
10_1101-436634	593	14	Cancer	Cancer	NNP
10_1101-436634	593	15	.	.	.
10_1101-436634	594	1	EBioMedicine	EBioMedicine	NNP
10_1101-436634	594	2	8	8	CD
10_1101-436634	594	3	,	,	,
10_1101-436634	594	4	30–39	30–39	CD
10_1101-436634	594	5	(	(	-LRB-
10_1101-436634	594	6	2016	2016	CD
10_1101-436634	594	7	)	)	-RRB-
10_1101-436634	594	8	.	.	.
10_1101-436634	595	1	44	44	CD
10_1101-436634	595	2	.	.	.
10_1101-436634	596	1	Gump	Gump	NNP
10_1101-436634	596	2	,	,	,
10_1101-436634	596	3	J.	J.	NNP
10_1101-436634	596	4	,	,	,
10_1101-436634	596	5	Stokoe	Stokoe	NNP
10_1101-436634	596	6	,	,	,
10_1101-436634	596	7	D.	D.	NNP
10_1101-436634	596	8	&	&	CC
10_1101-436634	596	9	McCormick	McCormick	NNP
10_1101-436634	596	10	,	,	,
10_1101-436634	596	11	F.	F.	NNP
10_1101-436634	596	12	Phosphorylation	Phosphorylation	NNP
10_1101-436634	596	13	of	of	IN
10_1101-436634	596	14	p16	p16	NN
10_1101-436634	596	15	INK4A	ink4a	NN
10_1101-436634	596	16	Correlates	Correlates	NNPS
10_1101-436634	596	17	with	with	IN
10_1101-436634	596	18	Cdk4	Cdk4	NNP
10_1101-436634	596	19	Association	Association	NNP
10_1101-436634	596	20	.	.	.
10_1101-436634	597	1	J.	J.	NNP
10_1101-436634	597	2	Biol	Biol	NNP
10_1101-436634	597	3	.	.	.
10_1101-436634	598	1	Chem	Chem	NNP
10_1101-436634	598	2	.	.	.
10_1101-436634	599	1	278	278	CD
10_1101-436634	599	2	,	,	,
10_1101-436634	599	3	6619–6622	6619–6622	CD
10_1101-436634	599	4	(	(	-LRB-
10_1101-436634	599	5	2003	2003	CD
10_1101-436634	599	6	)	)	-RRB-
10_1101-436634	599	7	.	.	.
10_1101-436634	600	1	45	45	CD
10_1101-436634	600	2	.	.	.
10_1101-436634	601	1	Quinlan	Quinlan	NNP
10_1101-436634	601	2	,	,	,
10_1101-436634	601	3	A.	A.	NNP
10_1101-436634	601	4	R.	R.	NNP
10_1101-436634	601	5	BEDTools	bedtool	NNS
10_1101-436634	601	6	:	:	:
10_1101-436634	601	7	The	the	DT
10_1101-436634	601	8	Swiss	Swiss	NNP
10_1101-436634	601	9	-	-	HYPH
10_1101-436634	601	10	Army	Army	NNP
10_1101-436634	601	11	Tool	Tool	NNP
10_1101-436634	601	12	for	for	IN
10_1101-436634	601	13	Genome	Genome	NNP
10_1101-436634	601	14	Feature	Feature	NNP
10_1101-436634	601	15	Analysis	Analysis	NNP
10_1101-436634	601	16	.	.	.
10_1101-436634	602	1	Curr	curr	UH
10_1101-436634	602	2	.	.	.
10_1101-436634	603	1	Protoc	Protoc	NNP
10_1101-436634	603	2	.	.	.
10_1101-436634	604	1	Bioinformatics	Bioinformatics	NNP
10_1101-436634	604	2	47	47	CD
10_1101-436634	604	3	,	,	,
10_1101-436634	604	4	11.12.1–34	11.12.1–34	CD
10_1101-436634	604	5	(	(	-LRB-
10_1101-436634	604	6	2014	2014	CD
10_1101-436634	604	7	)	)	-RRB-
10_1101-436634	604	8	.	.	.
10_1101-436634	605	1	46	46	CD
10_1101-436634	605	2	.	.	.
10_1101-436634	606	1	Li	Li	NNP
10_1101-436634	606	2	,	,	,
10_1101-436634	606	3	H.	H.	NNP
10_1101-436634	606	4	Tabix	Tabix	NNP
10_1101-436634	606	5	:	:	:
10_1101-436634	606	6	fast	fast	JJ
10_1101-436634	606	7	retrieval	retrieval	NN
10_1101-436634	606	8	of	of	IN
10_1101-436634	606	9	sequence	sequence	NN
10_1101-436634	606	10	features	feature	VBZ
10_1101-436634	606	11	from	from	IN
10_1101-436634	606	12	generic	generic	JJ
10_1101-436634	606	13	TAB	TAB	NNP
10_1101-436634	606	14	-	-	HYPH
10_1101-436634	606	15	delimited	delimit	VBN
10_1101-436634	606	16	files	file	NNS
10_1101-436634	606	17	.	.	.
10_1101-436634	607	1	Bioinformatics	Bioinformatics	NNP
10_1101-436634	607	2	27	27	CD
10_1101-436634	607	3	,	,	,
10_1101-436634	607	4	718–719	718–719	CD
10_1101-436634	607	5	(	(	-LRB-
10_1101-436634	607	6	2011	2011	CD
10_1101-436634	607	7	)	)	-RRB-
10_1101-436634	607	8	.	.	.
10_1101-436634	608	1	47	47	CD
10_1101-436634	608	2	.	.	.
10_1101-436634	609	1	GDC	GDC	NNP
10_1101-436634	609	2	Data	Data	NNP
10_1101-436634	609	3	Processing	Processing	NNP
10_1101-436634	609	4	.	.	.
10_1101-436634	610	1	https://gdc.cancer.gov/about-data/gdc-data-processing	https://gdc.cancer.gov/about-data/gdc-data-processing	NN
10_1101-436634	610	2	.	.	.
10_1101-436634	611	1	48	48	CD
10_1101-436634	611	2	.	.	.
10_1101-436634	612	1	Fan	Fan	NNP
10_1101-436634	612	2	,	,	,
10_1101-436634	612	3	Y.	Y.	NNP
10_1101-436634	612	4	et	et	NNP
10_1101-436634	612	5	al	al	NNP
10_1101-436634	612	6	.	.	.
10_1101-436634	613	1	Accounting	account	VBG
10_1101-436634	613	2	for	for	IN
10_1101-436634	613	3	tumor	tumor	NN
10_1101-436634	613	4	heterogeneity	heterogeneity	NN
10_1101-436634	613	5	using	use	VBG
10_1101-436634	613	6	a	a	DT
10_1101-436634	613	7	sample	sample	NN
10_1101-436634	613	8	-	-	HYPH
10_1101-436634	613	9	specific	specific	JJ
10_1101-436634	613	10	error	error	NN
10_1101-436634	613	11	model	model	NN
10_1101-436634	613	12	improves	improve	VBZ
10_1101-436634	613	13	sensitivity	sensitivity	NN
10_1101-436634	613	14	and	and	CC
10_1101-436634	613	15	specificity	specificity	NN
10_1101-436634	613	16	in	in	IN
10_1101-436634	613	17	mutation	mutation	NN
10_1101-436634	613	18	calling	call	VBG
10_1101-436634	613	19	for	for	IN
10_1101-436634	613	20	sequencing	sequence	VBG
10_1101-436634	613	21	data	datum	NNS
10_1101-436634	613	22	.	.	.
10_1101-436634	614	1	bioRxiv	biorxiv	IN
10_1101-436634	614	2	055467	055467	CD
10_1101-436634	614	3	(	(	-LRB-
10_1101-436634	614	4	2016	2016	CD
10_1101-436634	614	5	)	)	-RRB-
10_1101-436634	614	6	doi:10.1101/055467	doi:10.1101/055467	NN
10_1101-436634	614	7	.	.	.
10_1101-436634	615	1	49	49	CD
10_1101-436634	615	2	.	.	.
10_1101-436634	616	1	Cibulskis	Cibulskis	NNP
10_1101-436634	616	2	,	,	,
10_1101-436634	616	3	K.	K.	NNP
10_1101-436634	616	4	et	et	NNP
10_1101-436634	616	5	al	al	NNP
10_1101-436634	616	6	.	.	.
10_1101-436634	617	1	Sensitive	sensitive	JJ
10_1101-436634	617	2	detection	detection	NN
10_1101-436634	617	3	of	of	IN
10_1101-436634	617	4	somatic	somatic	JJ
10_1101-436634	617	5	point	point	NN
10_1101-436634	617	6	mutations	mutation	NNS
10_1101-436634	617	7	in	in	IN
10_1101-436634	617	8	impure	impure	NN
10_1101-436634	617	9	and	and	CC
10_1101-436634	617	10	heterogeneous	heterogeneous	JJ
10_1101-436634	617	11	cancer	cancer	NN
10_1101-436634	617	12	samples	sample	NNS
10_1101-436634	617	13	.	.	.
10_1101-436634	618	1	Nat	Nat	NNP
10_1101-436634	618	2	.	.	.
10_1101-436634	619	1	Biotechnol	Biotechnol	NNS
10_1101-436634	619	2	.	.	.
10_1101-436634	620	1	31	31	CD
10_1101-436634	620	2	,	,	,
10_1101-436634	620	3	213–219	213–219	CD
10_1101-436634	620	4	(	(	-LRB-
10_1101-436634	620	5	2013	2013	CD
10_1101-436634	620	6	)	)	-RRB-
10_1101-436634	620	7	.	.	.
10_1101-436634	621	1	.CC	.CC	NFP
10_1101-436634	621	2	-	-	:
10_1101-436634	621	3	BY	by	IN
10_1101-436634	621	4	-	-	HYPH
10_1101-436634	621	5	NC	NC	NNP
10_1101-436634	621	6	-	-	HYPH
10_1101-436634	621	7	ND	ND	NNP
10_1101-436634	621	8	4.0	4.0	CD
10_1101-436634	621	9	International	international	JJ
10_1101-436634	621	10	licensea	licensea	NNS
10_1101-436634	621	11	certified	certify	VBN
10_1101-436634	621	12	by	by	IN
10_1101-436634	621	13	peer	peer	NN
10_1101-436634	621	14	review	review	NN
10_1101-436634	621	15	)	)	-RRB-
10_1101-436634	621	16	is	be	VBZ
10_1101-436634	621	17	the	the	DT
10_1101-436634	621	18	author	author	NN
10_1101-436634	621	19	/	/	SYM
10_1101-436634	621	20	funder	funder	NN
10_1101-436634	621	21	,	,	,
10_1101-436634	621	22	who	who	WP
10_1101-436634	621	23	has	have	VBZ
10_1101-436634	621	24	granted	grant	VBN
10_1101-436634	621	25	bioRxiv	biorxiv	IN
10_1101-436634	621	26	a	a	DT
10_1101-436634	621	27	license	license	NN
10_1101-436634	621	28	to	to	TO
10_1101-436634	621	29	display	display	VB
10_1101-436634	621	30	the	the	DT
10_1101-436634	621	31	preprint	preprint	NN
10_1101-436634	621	32	in	in	IN
10_1101-436634	621	33	perpetuity	perpetuity	NN
10_1101-436634	621	34	.	.	.
10_1101-436634	622	1	It	-PRON-	PRP
10_1101-436634	622	2	is	be	VBZ
10_1101-436634	622	3	made	make	VBN
10_1101-436634	622	4	available	available	JJ
10_1101-436634	622	5	under	under	IN
10_1101-436634	622	6	The	the	DT
10_1101-436634	622	7	copyright	copyright	NN
10_1101-436634	622	8	holder	holder	NN
10_1101-436634	622	9	for	for	IN
10_1101-436634	622	10	this	this	DT
10_1101-436634	622	11	preprint	preprint	NN
10_1101-436634	622	12	(	(	-LRB-
10_1101-436634	622	13	which	which	WDT
10_1101-436634	622	14	was	be	VBD
10_1101-436634	622	15	notthis	notthis	DT
10_1101-436634	622	16	version	version	NN
10_1101-436634	622	17	posted	post	VBN
10_1101-436634	622	18	January	January	NNP
10_1101-436634	622	19	5	5	CD
10_1101-436634	622	20	,	,	,
10_1101-436634	622	21	2021	2021	CD
10_1101-436634	622	22	.	.	.
10_1101-436634	622	23	;	;	:
10_1101-436634	622	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	622	25	:	:	:
10_1101-436634	622	26	bioRxiv	biorxiv	VB
10_1101-436634	622	27	preprint	preprint	NN
10_1101-436634	622	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	622	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	CD
10_1101-436634	622	30	22	22	CD
10_1101-436634	622	31	50	50	CD
10_1101-436634	622	32	.	.	.
10_1101-436634	623	1	Koboldt	Koboldt	NNP
10_1101-436634	623	2	,	,	,
10_1101-436634	623	3	D.	D.	NNP
10_1101-436634	623	4	C.	C.	NNP
10_1101-436634	623	5	et	et	NNP
10_1101-436634	623	6	al	al	NNP
10_1101-436634	623	7	.	.	.
10_1101-436634	624	1	VarScan	VarScan	NNP
10_1101-436634	624	2	2	2	CD
10_1101-436634	624	3	:	:	:
10_1101-436634	624	4	somatic	somatic	JJ
10_1101-436634	624	5	mutation	mutation	NN
10_1101-436634	624	6	and	and	CC
10_1101-436634	624	7	copy	copy	NN
10_1101-436634	624	8	number	number	NN
10_1101-436634	624	9	alteration	alteration	NN
10_1101-436634	624	10	discovery	discovery	NN
10_1101-436634	624	11	in	in	IN
10_1101-436634	624	12	cancer	cancer	NN
10_1101-436634	624	13	by	by	IN
10_1101-436634	624	14	exome	exome	NNP
10_1101-436634	624	15	sequencing	sequencing	NN
10_1101-436634	624	16	.	.	.
10_1101-436634	625	1	Genome	Genome	NNP
10_1101-436634	625	2	Res	Res	NNP
10_1101-436634	625	3	.	.	.
10_1101-436634	626	1	22	22	CD
10_1101-436634	626	2	,	,	,
10_1101-436634	626	3	568–576	568–576	CD
10_1101-436634	626	4	(	(	-LRB-
10_1101-436634	626	5	2012	2012	CD
10_1101-436634	626	6	)	)	-RRB-
10_1101-436634	626	7	.	.	.
10_1101-436634	627	1	51	51	CD
10_1101-436634	627	2	.	.	.
10_1101-436634	628	1	Larson	Larson	NNP
10_1101-436634	628	2	,	,	,
10_1101-436634	628	3	D.	D.	NNP
10_1101-436634	628	4	E.	E.	NNP
10_1101-436634	628	5	et	et	NNP
10_1101-436634	628	6	al	al	NNP
10_1101-436634	628	7	.	.	.
10_1101-436634	629	1	SomaticSniper	SomaticSniper	NNP
10_1101-436634	629	2	:	:	:
10_1101-436634	629	3	identification	identification	NN
10_1101-436634	629	4	of	of	IN
10_1101-436634	629	5	somatic	somatic	JJ
10_1101-436634	629	6	point	point	NN
10_1101-436634	629	7	mutations	mutation	NNS
10_1101-436634	629	8	in	in	IN
10_1101-436634	629	9	whole	whole	JJ
10_1101-436634	629	10	genome	genome	JJ
10_1101-436634	629	11	sequencing	sequencing	NN
10_1101-436634	629	12	data	datum	NNS
10_1101-436634	629	13	.	.	.
10_1101-436634	630	1	Bioinformatics	Bioinformatics	NNP
10_1101-436634	630	2	28	28	CD
10_1101-436634	630	3	,	,	,
10_1101-436634	630	4	311–317	311–317	CD
10_1101-436634	630	5	(	(	-LRB-
10_1101-436634	630	6	2012	2012	CD
10_1101-436634	630	7	)	)	-RRB-
10_1101-436634	630	8	.	.	.
10_1101-436634	631	1	52	52	CD
10_1101-436634	631	2	.	.	.
10_1101-436634	632	1	Griffith	Griffith	NNP
10_1101-436634	632	2	,	,	,
10_1101-436634	632	3	M.	M.	NNP
10_1101-436634	632	4	et	et	NNP
10_1101-436634	632	5	al	al	NNP
10_1101-436634	632	6	.	.	.
10_1101-436634	633	1	Genome	Genome	NNP
10_1101-436634	633	2	Modeling	modeling	NN
10_1101-436634	633	3	System	system	NN
10_1101-436634	633	4	:	:	:
10_1101-436634	633	5	A	a	DT
10_1101-436634	633	6	Knowledge	Knowledge	NNP
10_1101-436634	633	7	Management	Management	NNP
10_1101-436634	633	8	Platform	Platform	NNP
10_1101-436634	633	9	for	for	IN
10_1101-436634	633	10	Genomics	Genomics	NNP
10_1101-436634	633	11	.	.	.
10_1101-436634	634	1	PLoS	PLoS	:
10_1101-436634	634	2	Comput	Comput	NNP
10_1101-436634	634	3	.	.	.
10_1101-436634	635	1	Biol	Biol	NNP
10_1101-436634	635	2	.	.	.
10_1101-436634	636	1	11	11	CD
10_1101-436634	636	2	,	,	,
10_1101-436634	636	3	e1004274	e1004274	NNP
10_1101-436634	636	4	(	(	-LRB-
10_1101-436634	636	5	2015	2015	CD
10_1101-436634	636	6	)	)	-RRB-
10_1101-436634	636	7	.	.	.
10_1101-436634	637	1	53	53	CD
10_1101-436634	637	2	.	.	.
10_1101-436634	638	1	Li	Li	NNP
10_1101-436634	638	2	,	,	,
10_1101-436634	638	3	H.	H.	NNP
10_1101-436634	638	4	&	&	CC
10_1101-436634	638	5	Durbin	Durbin	NNP
10_1101-436634	638	6	,	,	,
10_1101-436634	638	7	R.	R.	NNP
10_1101-436634	638	8	Fast	Fast	NNP
10_1101-436634	638	9	and	and	CC
10_1101-436634	638	10	accurate	accurate	JJ
10_1101-436634	638	11	short	short	JJ
10_1101-436634	638	12	read	read	NN
10_1101-436634	638	13	alignment	alignment	NN
10_1101-436634	638	14	with	with	IN
10_1101-436634	638	15	Burrows	Burrows	NNP
10_1101-436634	638	16	-	-	HYPH
10_1101-436634	638	17	Wheeler	Wheeler	NNP
10_1101-436634	638	18	transform	transform	NN
10_1101-436634	638	19	.	.	.
10_1101-436634	639	1	Bioinformatics	Bioinformatics	NNP
10_1101-436634	639	2	25	25	CD
10_1101-436634	639	3	,	,	,
10_1101-436634	639	4	1754–1760	1754–1760	CD
10_1101-436634	639	5	(	(	-LRB-
10_1101-436634	639	6	2009	2009	CD
10_1101-436634	639	7	)	)	-RRB-
10_1101-436634	639	8	.	.	.
10_1101-436634	640	1	54	54	CD
10_1101-436634	640	2	.	.	.
10_1101-436634	641	1	Saunders	Saunders	NNP
10_1101-436634	641	2	,	,	,
10_1101-436634	641	3	C.	C.	NNP
10_1101-436634	641	4	T.	T.	NNP
10_1101-436634	641	5	et	et	NNP
10_1101-436634	641	6	al	al	NNP
10_1101-436634	641	7	.	.	.
10_1101-436634	642	1	Strelka	strelka	NN
10_1101-436634	642	2	:	:	:
10_1101-436634	642	3	accurate	accurate	JJ
10_1101-436634	642	4	somatic	somatic	JJ
10_1101-436634	642	5	small	small	JJ
10_1101-436634	642	6	-	-	HYPH
10_1101-436634	642	7	variant	variant	JJ
10_1101-436634	642	8	calling	calling	NN
10_1101-436634	642	9	from	from	IN
10_1101-436634	642	10	sequenced	sequenced	JJ
10_1101-436634	642	11	tumor	tumor	NN
10_1101-436634	642	12	–	–	:
10_1101-436634	642	13	normal	normal	JJ
10_1101-436634	642	14	sample	sample	NN
10_1101-436634	642	15	pairs	pair	NNS
10_1101-436634	642	16	.	.	.
10_1101-436634	643	1	Bioinformatics	Bioinformatics	NNP
10_1101-436634	643	2	28	28	CD
10_1101-436634	643	3	,	,	,
10_1101-436634	643	4	1811–1817	1811–1817	CD
10_1101-436634	643	5	(	(	-LRB-
10_1101-436634	643	6	2012	2012	CD
10_1101-436634	643	7	)	)	-RRB-
10_1101-436634	643	8	.	.	.
10_1101-436634	644	1	.CC	.CC	NFP
10_1101-436634	644	2	-	-	:
10_1101-436634	644	3	BY	by	IN
10_1101-436634	644	4	-	-	HYPH
10_1101-436634	644	5	NC	NC	NNP
10_1101-436634	644	6	-	-	HYPH
10_1101-436634	644	7	ND	ND	NNP
10_1101-436634	644	8	4.0	4.0	CD
10_1101-436634	644	9	International	international	JJ
10_1101-436634	644	10	licensea	licensea	NNS
10_1101-436634	644	11	certified	certify	VBN
10_1101-436634	644	12	by	by	IN
10_1101-436634	644	13	peer	peer	NN
10_1101-436634	644	14	review	review	NN
10_1101-436634	644	15	)	)	-RRB-
10_1101-436634	644	16	is	be	VBZ
10_1101-436634	644	17	the	the	DT
10_1101-436634	644	18	author	author	NN
10_1101-436634	644	19	/	/	SYM
10_1101-436634	644	20	funder	funder	NN
10_1101-436634	644	21	,	,	,
10_1101-436634	644	22	who	who	WP
10_1101-436634	644	23	has	have	VBZ
10_1101-436634	644	24	granted	grant	VBN
10_1101-436634	644	25	bioRxiv	biorxiv	IN
10_1101-436634	644	26	a	a	DT
10_1101-436634	644	27	license	license	NN
10_1101-436634	644	28	to	to	TO
10_1101-436634	644	29	display	display	VB
10_1101-436634	644	30	the	the	DT
10_1101-436634	644	31	preprint	preprint	NN
10_1101-436634	644	32	in	in	IN
10_1101-436634	644	33	perpetuity	perpetuity	NN
10_1101-436634	644	34	.	.	.
10_1101-436634	645	1	It	-PRON-	PRP
10_1101-436634	645	2	is	be	VBZ
10_1101-436634	645	3	made	make	VBN
10_1101-436634	645	4	available	available	JJ
10_1101-436634	645	5	under	under	IN
10_1101-436634	645	6	The	the	DT
10_1101-436634	645	7	copyright	copyright	NN
10_1101-436634	645	8	holder	holder	NN
10_1101-436634	645	9	for	for	IN
10_1101-436634	645	10	this	this	DT
10_1101-436634	645	11	preprint	preprint	NN
10_1101-436634	645	12	(	(	-LRB-
10_1101-436634	645	13	which	which	WDT
10_1101-436634	645	14	was	be	VBD
10_1101-436634	645	15	notthis	notthis	DT
10_1101-436634	645	16	version	version	NN
10_1101-436634	645	17	posted	post	VBN
10_1101-436634	645	18	January	January	NNP
10_1101-436634	645	19	5	5	CD
10_1101-436634	645	20	,	,	,
10_1101-436634	645	21	2021	2021	CD
10_1101-436634	645	22	.	.	.
10_1101-436634	645	23	;	;	:
10_1101-436634	645	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	645	25	:	:	:
10_1101-436634	645	26	bioRxiv	biorxiv	VB
10_1101-436634	645	27	preprint	preprint	NN
10_1101-436634	645	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	645	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	CD
10_1101-436634	645	30	23	23	CD
10_1101-436634	645	31	Main	Main	NNP
10_1101-436634	645	32	Figures	Figures	NNPS
10_1101-436634	645	33	Figure	figure	NN
10_1101-436634	645	34	1	1	CD
10_1101-436634	645	35	:	:	:
10_1101-436634	645	36	Flexible	flexible	JJ
10_1101-436634	645	37	,	,	,
10_1101-436634	645	38	streamlined	streamlined	JJ
10_1101-436634	645	39	discovery	discovery	NN
10_1101-436634	645	40	of	of	IN
10_1101-436634	645	41	cis	cis	NN
10_1101-436634	645	42	-	-	HYPH
10_1101-436634	645	43	acting	act	VBG
10_1101-436634	645	44	splice	splice	NN
10_1101-436634	645	45	variants	variant	NNS
10_1101-436634	645	46	with	with	IN
10_1101-436634	645	47	RegTools	RegTools	NNP
10_1101-436634	645	48	modules	module	NNS
10_1101-436634	645	49	and	and	CC
10_1101-436634	645	50	cis	cis	NN
10_1101-436634	645	51	-	-	HYPH
10_1101-436634	645	52	splice	splice	NN
10_1101-436634	645	53	-	-	HYPH
10_1101-436634	645	54	effects	effect	NNS
10_1101-436634	645	55	identify	identify	VBP
10_1101-436634	645	56	workflow	workflow	NN
10_1101-436634	645	57	.	.	.
10_1101-436634	646	1	A	a	LS
10_1101-436634	646	2	)	)	-RRB-
10_1101-436634	646	3	By	by	IN
10_1101-436634	646	4	default	default	NN
10_1101-436634	646	5	,	,	,
10_1101-436634	646	6	variants	variant	NNS
10_1101-436634	646	7	annotate	annotate	VBP
10_1101-436634	646	8	marks	mark	NNS
10_1101-436634	646	9	variants	variant	NNS
10_1101-436634	646	10	within	within	IN
10_1101-436634	646	11	3bp	3bp	NN
10_1101-436634	646	12	on	on	IN
10_1101-436634	646	13	the	the	DT
10_1101-436634	646	14	exonic	exonic	JJ
10_1101-436634	646	15	side	side	NN
10_1101-436634	646	16	and	and	CC
10_1101-436634	646	17	2bp	2bp	NN
10_1101-436634	646	18	on	on	IN
10_1101-436634	646	19	the	the	DT
10_1101-436634	646	20	intronic	intronic	JJ
10_1101-436634	646	21	side	side	NN
10_1101-436634	646	22	of	of	IN
10_1101-436634	646	23	an	an	DT
10_1101-436634	646	24	exon	exon	JJ
10_1101-436634	646	25	edge	edge	NN
10_1101-436634	646	26	as	as	IN
10_1101-436634	646	27	potentially	potentially	RB
10_1101-436634	646	28	splicing	splice	VBG
10_1101-436634	646	29	-	-	HYPH
10_1101-436634	646	30	relevant	relevant	JJ
10_1101-436634	646	31	.	.	.
10_1101-436634	647	1	This	this	DT
10_1101-436634	647	2	“	"	``
10_1101-436634	647	3	splice	splice	NN
10_1101-436634	647	4	variant	variant	JJ
10_1101-436634	647	5	window	window	NN
10_1101-436634	647	6	”	"	''
10_1101-436634	647	7	can	can	MD
10_1101-436634	647	8	be	be	VB
10_1101-436634	647	9	modified	modify	VBN
10_1101-436634	647	10	individually	individually	RB
10_1101-436634	647	11	for	for	IN
10_1101-436634	647	12	the	the	DT
10_1101-436634	647	13	exonic	exonic	JJ
10_1101-436634	647	14	side	side	NN
10_1101-436634	647	15	and	and	CC
10_1101-436634	647	16	intronic	intronic	JJ
10_1101-436634	647	17	side	side	NN
10_1101-436634	647	18	using	use	VBG
10_1101-436634	647	19	the	the	DT
10_1101-436634	647	20	“	"	``
10_1101-436634	647	21	-e	-e	FW
10_1101-436634	647	22	”	"	''
10_1101-436634	647	23	and	and	CC
10_1101-436634	647	24	“	"	``
10_1101-436634	647	25	-i	-i	:
10_1101-436634	647	26	”	"	''
10_1101-436634	647	27	options	option	NNS
10_1101-436634	647	28	,	,	,
10_1101-436634	647	29	respectively	respectively	RB
10_1101-436634	647	30	.	.	.
10_1101-436634	648	1	With	with	IN
10_1101-436634	648	2	cis	cis	NN
10_1101-436634	648	3	-	-	HYPH
10_1101-436634	648	4	splice	splice	NN
10_1101-436634	648	5	-	-	HYPH
10_1101-436634	648	6	effects	effect	NNS
10_1101-436634	648	7	identify	identify	VBP
10_1101-436634	648	8	,	,	,
10_1101-436634	648	9	for	for	IN
10_1101-436634	648	10	each	each	DT
10_1101-436634	648	11	variant	variant	NN
10_1101-436634	648	12	in	in	IN
10_1101-436634	648	13	the	the	DT
10_1101-436634	648	14	splice	splice	NN
10_1101-436634	648	15	variant	variant	JJ
10_1101-436634	648	16	window	window	NN
10_1101-436634	648	17	,	,	,
10_1101-436634	648	18	a	a	DT
10_1101-436634	648	19	“	"	``
10_1101-436634	648	20	splice	splice	NN
10_1101-436634	648	21	junction	junction	NN
10_1101-436634	648	22	region	region	NN
10_1101-436634	648	23	”	"	''
10_1101-436634	648	24	is	be	VBZ
10_1101-436634	648	25	determined	determine	VBN
10_1101-436634	648	26	by	by	IN
10_1101-436634	648	27	finding	find	VBG
10_1101-436634	648	28	the	the	DT
10_1101-436634	648	29	largest	large	JJS
10_1101-436634	648	30	span	span	NN
10_1101-436634	648	31	of	of	IN
10_1101-436634	648	32	sequence	sequence	NN
10_1101-436634	648	33	space	space	NN
10_1101-436634	648	34	between	between	IN
10_1101-436634	648	35	exons	exon	NNS
10_1101-436634	648	36	which	which	WDT
10_1101-436634	648	37	flank	flank	VBP
10_1101-436634	648	38	the	the	DT
10_1101-436634	648	39	exon	exon	NNS
10_1101-436634	648	40	associated	associate	VBN
10_1101-436634	648	41	with	with	IN
10_1101-436634	648	42	the	the	DT
10_1101-436634	648	43	splicing	splicing	NN
10_1101-436634	648	44	-	-	HYPH
10_1101-436634	648	45	relevant	relevant	JJ
10_1101-436634	648	46	variant	variant	NN
10_1101-436634	648	47	.	.	.
10_1101-436634	649	1	The	the	DT
10_1101-436634	649	2	splice	splice	NN
10_1101-436634	649	3	junction	junction	NN
10_1101-436634	649	4	region	region	NN
10_1101-436634	649	5	can	can	MD
10_1101-436634	649	6	also	also	RB
10_1101-436634	649	7	be	be	VB
10_1101-436634	649	8	set	set	VBN
10_1101-436634	649	9	manually	manually	RB
10_1101-436634	649	10	to	to	TO
10_1101-436634	649	11	contain	contain	VB
10_1101-436634	649	12	the	the	DT
10_1101-436634	649	13	entire	entire	JJ
10_1101-436634	649	14	sequence	sequence	NN
10_1101-436634	649	15	space	space	NN
10_1101-436634	649	16	n	n	CC
10_1101-436634	649	17	bases	basis	NNS
10_1101-436634	649	18	upstream	upstream	JJ
10_1101-436634	649	19	and	and	CC
10_1101-436634	649	20	downstream	downstream	JJ
10_1101-436634	649	21	of	of	IN
10_1101-436634	649	22	the	the	DT
10_1101-436634	649	23	variant	variant	NN
10_1101-436634	649	24	using	use	VBG
10_1101-436634	649	25	the	the	DT
10_1101-436634	649	26	“	"	``
10_1101-436634	649	27	-w	-w	NN
10_1101-436634	649	28	”	"	''
10_1101-436634	649	29	option	option	NN
10_1101-436634	649	30	.	.	.
10_1101-436634	650	1	Junctions	junction	NNS
10_1101-436634	650	2	overlapping	overlap	VBG
10_1101-436634	650	3	the	the	DT
10_1101-436634	650	4	splice	splice	NN
10_1101-436634	650	5	junction	junction	NN
10_1101-436634	650	6	region	region	NN
10_1101-436634	650	7	are	be	VBP
10_1101-436634	650	8	associated	associate	VBN
10_1101-436634	650	9	with	with	IN
10_1101-436634	650	10	the	the	DT
10_1101-436634	650	11	variant	variant	NN
10_1101-436634	650	12	.	.	.
10_1101-436634	651	1	Using	use	VBG
10_1101-436634	651	2	the	the	DT
10_1101-436634	651	3	-E	-E	HYPH
10_1101-436634	651	4	option	option	NN
10_1101-436634	651	5	considers	consider	VBZ
10_1101-436634	651	6	all	all	DT
10_1101-436634	651	7	exonic	exonic	JJ
10_1101-436634	651	8	variants	variant	NNS
10_1101-436634	651	9	as	as	IN
10_1101-436634	651	10	potentially	potentially	RB
10_1101-436634	651	11	splicing	splice	VBG
10_1101-436634	651	12	-	-	HYPH
10_1101-436634	651	13	relevant	relevant	JJ
10_1101-436634	651	14	,	,	,
10_1101-436634	651	15	but	but	CC
10_1101-436634	651	16	is	be	VBZ
10_1101-436634	651	17	otherwise	otherwise	RB
10_1101-436634	651	18	the	the	DT
10_1101-436634	651	19	same	same	JJ
10_1101-436634	651	20	.	.	.
10_1101-436634	652	1	The	the	DT
10_1101-436634	652	2	-I	-I	NNP
10_1101-436634	652	3	option	option	NN
10_1101-436634	652	4	considers	consider	VBZ
10_1101-436634	652	5	all	all	DT
10_1101-436634	652	6	intronic	intronic	JJ
10_1101-436634	652	7	variants	variant	NNS
10_1101-436634	652	8	and	and	CC
10_1101-436634	652	9	also	also	RB
10_1101-436634	652	10	limits	limit	VBZ
10_1101-436634	652	11	the	the	DT
10_1101-436634	652	12	splice	splice	NN
10_1101-436634	652	13	junction	junction	NN
10_1101-436634	652	14	region	region	NN
10_1101-436634	652	15	to	to	IN
10_1101-436634	652	16	the	the	DT
10_1101-436634	652	17	intronic	intronic	JJ
10_1101-436634	652	18	region	region	NN
10_1101-436634	652	19	in	in	IN
10_1101-436634	652	20	which	which	WDT
10_1101-436634	652	21	the	the	DT
10_1101-436634	652	22	variant	variant	NN
10_1101-436634	652	23	is	be	VBZ
10_1101-436634	652	24	found	find	VBN
10_1101-436634	652	25	,	,	,
10_1101-436634	652	26	excluding	exclude	VBG
10_1101-436634	652	27	the	the	DT
10_1101-436634	652	28	flanking	flank	VBG
10_1101-436634	652	29	exons	exon	NNS
10_1101-436634	652	30	.	.	.
10_1101-436634	653	1	B	B	NNP
10_1101-436634	653	2	)	)	-RRB-
10_1101-436634	653	3	Cis	Cis	NNP
10_1101-436634	653	4	-	-	HYPH
10_1101-436634	653	5	splice	splice	NN
10_1101-436634	653	6	-	-	HYPH
10_1101-436634	653	7	effects	effect	NNS
10_1101-436634	653	8	identify	identify	VBP
10_1101-436634	653	9	and	and	CC
10_1101-436634	653	10	the	the	DT
10_1101-436634	653	11	underlying	underlie	VBG
10_1101-436634	653	12	junctions	junction	NNS
10_1101-436634	653	13	annotate	annotate	JJ
10_1101-436634	653	14	command	command	NN
10_1101-436634	653	15	annotate	annotate	NN
10_1101-436634	653	16	splicing	splicing	NN
10_1101-436634	653	17	events	event	NNS
10_1101-436634	653	18	based	base	VBN
10_1101-436634	653	19	on	on	IN
10_1101-436634	653	20	whether	whether	IN
10_1101-436634	653	21	the	the	DT
10_1101-436634	653	22	donor	donor	NN
10_1101-436634	653	23	and	and	CC
10_1101-436634	653	24	acceptor	acceptor	NN
10_1101-436634	653	25	site	site	NN
10_1101-436634	653	26	combination	combination	NN
10_1101-436634	653	27	is	be	VBZ
10_1101-436634	653	28	found	find	VBN
10_1101-436634	653	29	in	in	IN
10_1101-436634	653	30	the	the	DT
10_1101-436634	653	31	reference	reference	NN
10_1101-436634	653	32	transcriptome	transcriptome	DT
10_1101-436634	653	33	GTF	GTF	NNP
10_1101-436634	653	34	.	.	.
10_1101-436634	654	1	In	in	IN
10_1101-436634	654	2	this	this	DT
10_1101-436634	654	3	example	example	NN
10_1101-436634	654	4	,	,	,
10_1101-436634	654	5	there	there	EX
10_1101-436634	654	6	are	be	VBP
10_1101-436634	654	7	two	two	CD
10_1101-436634	654	8	known	know	VBN
10_1101-436634	654	9	transcripts	transcript	NNS
10_1101-436634	654	10	(	(	-LRB-
10_1101-436634	654	11	shown	show	VBN
10_1101-436634	654	12	in	in	IN
10_1101-436634	654	13	blue	blue	NNP
10_1101-436634	654	14	)	)	-RRB-
10_1101-436634	654	15	which	which	WDT
10_1101-436634	654	16	overlap	overlap	VBP
10_1101-436634	654	17	a	a	DT
10_1101-436634	654	18	set	set	NN
10_1101-436634	654	19	of	of	IN
10_1101-436634	654	20	junctions	junction	NNS
10_1101-436634	654	21	from	from	IN
10_1101-436634	654	22	RNAseq	RNAseq	NNP
10_1101-436634	654	23	data	datum	NNS
10_1101-436634	654	24	(	(	-LRB-
10_1101-436634	654	25	depicted	depict	VBN
10_1101-436634	654	26	as	as	IN
10_1101-436634	654	27	junction	junction	NN
10_1101-436634	654	28	supporting	support	VBG
10_1101-436634	654	29	reads	read	NNS
10_1101-436634	654	30	.CC	.CC	:
10_1101-436634	654	31	-	-	:
10_1101-436634	654	32	BY	by	IN
10_1101-436634	654	33	-	-	HYPH
10_1101-436634	654	34	NC	NC	NNP
10_1101-436634	654	35	-	-	HYPH
10_1101-436634	654	36	ND	ND	NNP
10_1101-436634	654	37	4.0	4.0	CD
10_1101-436634	654	38	International	international	JJ
10_1101-436634	654	39	licensea	licensea	NNS
10_1101-436634	654	40	certified	certify	VBN
10_1101-436634	654	41	by	by	IN
10_1101-436634	654	42	peer	peer	NN
10_1101-436634	654	43	review	review	NN
10_1101-436634	654	44	)	)	-RRB-
10_1101-436634	654	45	is	be	VBZ
10_1101-436634	654	46	the	the	DT
10_1101-436634	654	47	author	author	NN
10_1101-436634	654	48	/	/	SYM
10_1101-436634	654	49	funder	funder	NN
10_1101-436634	654	50	,	,	,
10_1101-436634	654	51	who	who	WP
10_1101-436634	654	52	has	have	VBZ
10_1101-436634	654	53	granted	grant	VBN
10_1101-436634	654	54	bioRxiv	biorxiv	IN
10_1101-436634	654	55	a	a	DT
10_1101-436634	654	56	license	license	NN
10_1101-436634	654	57	to	to	TO
10_1101-436634	654	58	display	display	VB
10_1101-436634	654	59	the	the	DT
10_1101-436634	654	60	preprint	preprint	NN
10_1101-436634	654	61	in	in	IN
10_1101-436634	654	62	perpetuity	perpetuity	NN
10_1101-436634	654	63	.	.	.
10_1101-436634	655	1	It	-PRON-	PRP
10_1101-436634	655	2	is	be	VBZ
10_1101-436634	655	3	made	make	VBN
10_1101-436634	655	4	available	available	JJ
10_1101-436634	655	5	under	under	IN
10_1101-436634	655	6	The	the	DT
10_1101-436634	655	7	copyright	copyright	NN
10_1101-436634	655	8	holder	holder	NN
10_1101-436634	655	9	for	for	IN
10_1101-436634	655	10	this	this	DT
10_1101-436634	655	11	preprint	preprint	NN
10_1101-436634	655	12	(	(	-LRB-
10_1101-436634	655	13	which	which	WDT
10_1101-436634	655	14	was	be	VBD
10_1101-436634	655	15	notthis	notthis	DT
10_1101-436634	655	16	version	version	NN
10_1101-436634	655	17	posted	post	VBN
10_1101-436634	655	18	January	January	NNP
10_1101-436634	655	19	5	5	CD
10_1101-436634	655	20	,	,	,
10_1101-436634	655	21	2021	2021	CD
10_1101-436634	655	22	.	.	.
10_1101-436634	655	23	;	;	:
10_1101-436634	655	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	655	25	:	:	:
10_1101-436634	655	26	bioRxiv	biorxiv	VB
10_1101-436634	655	27	preprint	preprint	NN
10_1101-436634	655	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	655	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	RB
10_1101-436634	655	30	24	24	CD
10_1101-436634	655	31	in	in	IN
10_1101-436634	655	32	red	red	NN
10_1101-436634	655	33	)	)	-RRB-
10_1101-436634	655	34	.	.	.
10_1101-436634	656	1	Comparing	compare	VBG
10_1101-436634	656	2	the	the	DT
10_1101-436634	656	3	observed	observed	JJ
10_1101-436634	656	4	junctions	junction	NNS
10_1101-436634	656	5	to	to	IN
10_1101-436634	656	6	the	the	DT
10_1101-436634	656	7	reference	reference	NN
10_1101-436634	656	8	junctions	junction	NNS
10_1101-436634	656	9	in	in	IN
10_1101-436634	656	10	the	the	DT
10_1101-436634	656	11	first	first	JJ
10_1101-436634	656	12	transcript	transcript	NN
10_1101-436634	656	13	(	(	-LRB-
10_1101-436634	656	14	top	top	JJ
10_1101-436634	656	15	panel	panel	NN
10_1101-436634	656	16	)	)	-RRB-
10_1101-436634	656	17	,	,	,
10_1101-436634	656	18	RegTools	RegTools	NNP
10_1101-436634	656	19	checks	check	NNS
10_1101-436634	656	20	to	to	TO
10_1101-436634	656	21	see	see	VB
10_1101-436634	656	22	if	if	IN
10_1101-436634	656	23	the	the	DT
10_1101-436634	656	24	observed	observed	JJ
10_1101-436634	656	25	donor	donor	NN
10_1101-436634	656	26	and	and	CC
10_1101-436634	656	27	acceptor	acceptor	NN
10_1101-436634	656	28	splice	splice	NN
10_1101-436634	656	29	sites	site	NNS
10_1101-436634	656	30	are	be	VBP
10_1101-436634	656	31	found	find	VBN
10_1101-436634	656	32	in	in	IN
10_1101-436634	656	33	any	any	DT
10_1101-436634	656	34	of	of	IN
10_1101-436634	656	35	the	the	DT
10_1101-436634	656	36	reference	reference	NN
10_1101-436634	656	37	exons	exon	NNS
10_1101-436634	656	38	and	and	CC
10_1101-436634	656	39	also	also	RB
10_1101-436634	656	40	counts	count	VBZ
10_1101-436634	656	41	the	the	DT
10_1101-436634	656	42	number	number	NN
10_1101-436634	656	43	of	of	IN
10_1101-436634	656	44	exons	exon	NNS
10_1101-436634	656	45	,	,	,
10_1101-436634	656	46	acceptors	acceptor	NNS
10_1101-436634	656	47	,	,	,
10_1101-436634	656	48	and	and	CC
10_1101-436634	656	49	donors	donor	NNS
10_1101-436634	656	50	skipped	skip	VBN
10_1101-436634	656	51	by	by	IN
10_1101-436634	656	52	a	a	DT
10_1101-436634	656	53	particular	particular	JJ
10_1101-436634	656	54	junction	junction	NN
10_1101-436634	656	55	.	.	.
10_1101-436634	657	1	Double	double	JJ
10_1101-436634	657	2	arrows	arrow	NNS
10_1101-436634	657	3	represent	represent	VBP
10_1101-436634	657	4	matches	match	NNS
10_1101-436634	657	5	between	between	IN
10_1101-436634	657	6	observed	observed	JJ
10_1101-436634	657	7	and	and	CC
10_1101-436634	657	8	reference	reference	NN
10_1101-436634	657	9	acceptor	acceptor	NN
10_1101-436634	657	10	/	/	SYM
10_1101-436634	657	11	donor	donor	NN
10_1101-436634	657	12	sites	site	NNS
10_1101-436634	657	13	while	while	IN
10_1101-436634	657	14	single	single	JJ
10_1101-436634	657	15	arrows	arrow	NNS
10_1101-436634	657	16	show	show	VBP
10_1101-436634	657	17	novel	novel	JJ
10_1101-436634	657	18	splice	splice	NN
10_1101-436634	657	19	sites	site	NNS
10_1101-436634	657	20	.	.	.
10_1101-436634	658	1	These	these	DT
10_1101-436634	658	2	steps	step	NNS
10_1101-436634	658	3	are	be	VBP
10_1101-436634	658	4	repeated	repeat	VBN
10_1101-436634	658	5	for	for	IN
10_1101-436634	658	6	the	the	DT
10_1101-436634	658	7	rest	rest	NN
10_1101-436634	658	8	of	of	IN
10_1101-436634	658	9	the	the	DT
10_1101-436634	658	10	relevant	relevant	JJ
10_1101-436634	658	11	transcripts	transcript	NNS
10_1101-436634	658	12	,	,	,
10_1101-436634	658	13	keeping	keep	VBG
10_1101-436634	658	14	track	track	NN
10_1101-436634	658	15	of	of	IN
10_1101-436634	658	16	whether	whether	IN
10_1101-436634	658	17	there	there	EX
10_1101-436634	658	18	are	be	VBP
10_1101-436634	658	19	known	know	VBN
10_1101-436634	658	20	acceptor	acceptor	NN
10_1101-436634	658	21	-	-	HYPH
10_1101-436634	658	22	donor	donor	NN
10_1101-436634	658	23	combinations	combination	NNS
10_1101-436634	658	24	.	.	.
10_1101-436634	659	1	Junctions	junction	NNS
10_1101-436634	659	2	with	with	IN
10_1101-436634	659	3	a	a	DT
10_1101-436634	659	4	known	know	VBN
10_1101-436634	659	5	donor	donor	NN
10_1101-436634	659	6	but	but	CC
10_1101-436634	659	7	novel	novel	JJ
10_1101-436634	659	8	acceptor	acceptor	NN
10_1101-436634	659	9	or	or	CC
10_1101-436634	659	10	vice	vice	NN
10_1101-436634	659	11	-	-	HYPH
10_1101-436634	659	12	versa	versa	JJ
10_1101-436634	659	13	are	be	VBP
10_1101-436634	659	14	annotated	annotate	VBN
10_1101-436634	659	15	as	as	IN
10_1101-436634	659	16	“	"	``
10_1101-436634	659	17	D	D	NNP
10_1101-436634	659	18	”	"	''
10_1101-436634	659	19	or	or	CC
10_1101-436634	659	20	“	"	``
10_1101-436634	659	21	A	a	NN
10_1101-436634	659	22	”	"	''
10_1101-436634	659	23	,	,	,
10_1101-436634	659	24	respectively	respectively	RB
10_1101-436634	659	25	.	.	.
10_1101-436634	660	1	If	if	IN
10_1101-436634	660	2	both	both	DT
10_1101-436634	660	3	sites	site	NNS
10_1101-436634	660	4	are	be	VBP
10_1101-436634	660	5	known	know	VBN
10_1101-436634	660	6	but	but	CC
10_1101-436634	660	7	do	do	VBP
10_1101-436634	660	8	not	not	RB
10_1101-436634	660	9	appear	appear	VB
10_1101-436634	660	10	in	in	IN
10_1101-436634	660	11	combination	combination	NN
10_1101-436634	660	12	in	in	IN
10_1101-436634	660	13	any	any	DT
10_1101-436634	660	14	transcripts	transcript	NNS
10_1101-436634	660	15	,	,	,
10_1101-436634	660	16	the	the	DT
10_1101-436634	660	17	junction	junction	NN
10_1101-436634	660	18	is	be	VBZ
10_1101-436634	660	19	annotated	annotate	VBN
10_1101-436634	660	20	as	as	IN
10_1101-436634	660	21	“	"	``
10_1101-436634	660	22	NDA	NDA	NNP
10_1101-436634	660	23	”	"	''
10_1101-436634	660	24	,	,	,
10_1101-436634	660	25	whereas	whereas	IN
10_1101-436634	660	26	if	if	IN
10_1101-436634	660	27	both	both	DT
10_1101-436634	660	28	sites	site	NNS
10_1101-436634	660	29	are	be	VBP
10_1101-436634	660	30	unknown	unknown	JJ
10_1101-436634	660	31	,	,	,
10_1101-436634	660	32	the	the	DT
10_1101-436634	660	33	junction	junction	NN
10_1101-436634	660	34	is	be	VBZ
10_1101-436634	660	35	annotated	annotate	VBN
10_1101-436634	660	36	as	as	IN
10_1101-436634	660	37	“	"	``
10_1101-436634	660	38	N	N	NNP
10_1101-436634	660	39	”	"	''
10_1101-436634	660	40	.	.	.
10_1101-436634	661	1	If	if	IN
10_1101-436634	661	2	the	the	DT
10_1101-436634	661	3	junction	junction	NN
10_1101-436634	661	4	is	be	VBZ
10_1101-436634	661	5	known	know	VBN
10_1101-436634	661	6	to	to	IN
10_1101-436634	661	7	the	the	DT
10_1101-436634	661	8	reference	reference	NN
10_1101-436634	661	9	GTF	gtf	NN
10_1101-436634	661	10	,	,	,
10_1101-436634	661	11	it	-PRON-	PRP
10_1101-436634	661	12	is	be	VBZ
10_1101-436634	661	13	marked	mark	VBN
10_1101-436634	661	14	as	as	IN
10_1101-436634	661	15	“	"	``
10_1101-436634	661	16	DA	DA	NNP
10_1101-436634	661	17	”	"	''
10_1101-436634	661	18	.	.	.
10_1101-436634	662	1	C	C	NNP
10_1101-436634	662	2	)	)	-RRB-
10_1101-436634	662	3	The	the	DT
10_1101-436634	662	4	cis	cis	NN
10_1101-436634	662	5	-	-	HYPH
10_1101-436634	662	6	splice	splice	NN
10_1101-436634	662	7	-	-	HYPH
10_1101-436634	662	8	effects	effect	NNS
10_1101-436634	662	9	identify	identify	VBP
10_1101-436634	662	10	command	command	NN
10_1101-436634	662	11	relies	rely	VBZ
10_1101-436634	662	12	on	on	IN
10_1101-436634	662	13	the	the	DT
10_1101-436634	662	14	variants	variant	NNS
10_1101-436634	662	15	annotate	annotate	VBP
10_1101-436634	662	16	,	,	,
10_1101-436634	662	17	junctions	junction	NNS
10_1101-436634	662	18	extract	extract	NN
10_1101-436634	662	19	,	,	,
10_1101-436634	662	20	and	and	CC
10_1101-436634	662	21	junctions	junction	NNS
10_1101-436634	662	22	annotate	annotate	JJ
10_1101-436634	662	23	submodules	submodule	NNS
10_1101-436634	662	24	.	.	.
10_1101-436634	663	1	This	this	DT
10_1101-436634	663	2	pipeline	pipeline	NN
10_1101-436634	663	3	takes	take	VBZ
10_1101-436634	663	4	variant	variant	JJ
10_1101-436634	663	5	calls	call	NNS
10_1101-436634	663	6	and	and	CC
10_1101-436634	663	7	RNA	RNA	NNP
10_1101-436634	663	8	-	-	HYPH
10_1101-436634	663	9	seq	seq	NN
10_1101-436634	663	10	alignments	alignment	NNS
10_1101-436634	663	11	along	along	IN
10_1101-436634	663	12	with	with	IN
10_1101-436634	663	13	genome	genome	JJ
10_1101-436634	663	14	and	and	CC
10_1101-436634	663	15	transcriptome	transcriptome	DT
10_1101-436634	663	16	references	reference	NNS
10_1101-436634	663	17	and	and	CC
10_1101-436634	663	18	outputs	output	NNS
10_1101-436634	663	19	information	information	NN
10_1101-436634	663	20	about	about	IN
10_1101-436634	663	21	novel	novel	JJ
10_1101-436634	663	22	junctions	junction	NNS
10_1101-436634	663	23	and	and	CC
10_1101-436634	663	24	associated	associate	VBD
10_1101-436634	663	25	potential	potential	JJ
10_1101-436634	663	26	cis	cis	NN
10_1101-436634	663	27	splice	splice	NN
10_1101-436634	663	28	-	-	HYPH
10_1101-436634	663	29	altering	alter	VBG
10_1101-436634	663	30	sequence	sequence	NN
10_1101-436634	663	31	variants	variant	NNS
10_1101-436634	663	32	.	.	.
10_1101-436634	664	1	RegTools	RegTools	NNP
10_1101-436634	664	2	is	be	VBZ
10_1101-436634	664	3	agnostic	agnostic	JJ
10_1101-436634	664	4	to	to	TO
10_1101-436634	664	5	downstream	downstream	JJ
10_1101-436634	664	6	research	research	NN
10_1101-436634	664	7	goals	goal	NNS
10_1101-436634	664	8	and	and	CC
10_1101-436634	664	9	its	-PRON-	PRP$
10_1101-436634	664	10	output	output	NN
10_1101-436634	664	11	can	can	MD
10_1101-436634	664	12	be	be	VB
10_1101-436634	664	13	filtered	filter	VBN
10_1101-436634	664	14	through	through	IN
10_1101-436634	664	15	user	user	NN
10_1101-436634	664	16	-	-	HYPH
10_1101-436634	664	17	specific	specific	JJ
10_1101-436634	664	18	methods	method	NNS
10_1101-436634	664	19	and	and	CC
10_1101-436634	664	20	thus	thus	RB
10_1101-436634	664	21	can	can	MD
10_1101-436634	664	22	be	be	VB
10_1101-436634	664	23	applied	apply	VBN
10_1101-436634	664	24	to	to	IN
10_1101-436634	664	25	a	a	DT
10_1101-436634	664	26	broad	broad	JJ
10_1101-436634	664	27	set	set	NN
10_1101-436634	664	28	of	of	IN
10_1101-436634	664	29	scientific	scientific	JJ
10_1101-436634	664	30	questions	question	NNS
10_1101-436634	664	31	.	.	.
10_1101-436634	665	1	.CC	.CC	NFP
10_1101-436634	665	2	-	-	:
10_1101-436634	665	3	BY	by	IN
10_1101-436634	665	4	-	-	HYPH
10_1101-436634	665	5	NC	NC	NNP
10_1101-436634	665	6	-	-	HYPH
10_1101-436634	665	7	ND	ND	NNP
10_1101-436634	665	8	4.0	4.0	CD
10_1101-436634	665	9	International	international	JJ
10_1101-436634	665	10	licensea	licensea	NNS
10_1101-436634	665	11	certified	certify	VBN
10_1101-436634	665	12	by	by	IN
10_1101-436634	665	13	peer	peer	NN
10_1101-436634	665	14	review	review	NN
10_1101-436634	665	15	)	)	-RRB-
10_1101-436634	665	16	is	be	VBZ
10_1101-436634	665	17	the	the	DT
10_1101-436634	665	18	author	author	NN
10_1101-436634	665	19	/	/	SYM
10_1101-436634	665	20	funder	funder	NN
10_1101-436634	665	21	,	,	,
10_1101-436634	665	22	who	who	WP
10_1101-436634	665	23	has	have	VBZ
10_1101-436634	665	24	granted	grant	VBN
10_1101-436634	665	25	bioRxiv	biorxiv	IN
10_1101-436634	665	26	a	a	DT
10_1101-436634	665	27	license	license	NN
10_1101-436634	665	28	to	to	TO
10_1101-436634	665	29	display	display	VB
10_1101-436634	665	30	the	the	DT
10_1101-436634	665	31	preprint	preprint	NN
10_1101-436634	665	32	in	in	IN
10_1101-436634	665	33	perpetuity	perpetuity	NN
10_1101-436634	665	34	.	.	.
10_1101-436634	666	1	It	-PRON-	PRP
10_1101-436634	666	2	is	be	VBZ
10_1101-436634	666	3	made	make	VBN
10_1101-436634	666	4	available	available	JJ
10_1101-436634	666	5	under	under	IN
10_1101-436634	666	6	The	the	DT
10_1101-436634	666	7	copyright	copyright	NN
10_1101-436634	666	8	holder	holder	NN
10_1101-436634	666	9	for	for	IN
10_1101-436634	666	10	this	this	DT
10_1101-436634	666	11	preprint	preprint	NN
10_1101-436634	666	12	(	(	-LRB-
10_1101-436634	666	13	which	which	WDT
10_1101-436634	666	14	was	be	VBD
10_1101-436634	666	15	notthis	notthis	DT
10_1101-436634	666	16	version	version	NN
10_1101-436634	666	17	posted	post	VBN
10_1101-436634	666	18	January	January	NNP
10_1101-436634	666	19	5	5	CD
10_1101-436634	666	20	,	,	,
10_1101-436634	666	21	2021	2021	CD
10_1101-436634	666	22	.	.	.
10_1101-436634	666	23	;	;	:
10_1101-436634	666	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	666	25	:	:	:
10_1101-436634	666	26	bioRxiv	biorxiv	VB
10_1101-436634	666	27	preprint	preprint	NN
10_1101-436634	666	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	666	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	666	30	25	25	CD
10_1101-436634	666	31	.CC	.CC	:
10_1101-436634	666	32	-	-	HYPH
10_1101-436634	666	33	BY	by	IN
10_1101-436634	666	34	-	-	HYPH
10_1101-436634	666	35	NC	NC	NNP
10_1101-436634	666	36	-	-	HYPH
10_1101-436634	666	37	ND	ND	NNP
10_1101-436634	666	38	4.0	4.0	CD
10_1101-436634	666	39	International	international	JJ
10_1101-436634	666	40	licensea	licensea	NNS
10_1101-436634	666	41	certified	certify	VBN
10_1101-436634	666	42	by	by	IN
10_1101-436634	666	43	peer	peer	NN
10_1101-436634	666	44	review	review	NN
10_1101-436634	666	45	)	)	-RRB-
10_1101-436634	666	46	is	be	VBZ
10_1101-436634	666	47	the	the	DT
10_1101-436634	666	48	author	author	NN
10_1101-436634	666	49	/	/	SYM
10_1101-436634	666	50	funder	funder	NN
10_1101-436634	666	51	,	,	,
10_1101-436634	666	52	who	who	WP
10_1101-436634	666	53	has	have	VBZ
10_1101-436634	666	54	granted	grant	VBN
10_1101-436634	666	55	bioRxiv	biorxiv	IN
10_1101-436634	666	56	a	a	DT
10_1101-436634	666	57	license	license	NN
10_1101-436634	666	58	to	to	TO
10_1101-436634	666	59	display	display	VB
10_1101-436634	666	60	the	the	DT
10_1101-436634	666	61	preprint	preprint	NN
10_1101-436634	666	62	in	in	IN
10_1101-436634	666	63	perpetuity	perpetuity	NN
10_1101-436634	666	64	.	.	.
10_1101-436634	667	1	It	-PRON-	PRP
10_1101-436634	667	2	is	be	VBZ
10_1101-436634	667	3	made	make	VBN
10_1101-436634	667	4	available	available	JJ
10_1101-436634	667	5	under	under	IN
10_1101-436634	667	6	The	the	DT
10_1101-436634	667	7	copyright	copyright	NN
10_1101-436634	667	8	holder	holder	NN
10_1101-436634	667	9	for	for	IN
10_1101-436634	667	10	this	this	DT
10_1101-436634	667	11	preprint	preprint	NN
10_1101-436634	667	12	(	(	-LRB-
10_1101-436634	667	13	which	which	WDT
10_1101-436634	667	14	was	be	VBD
10_1101-436634	667	15	notthis	notthis	DT
10_1101-436634	667	16	version	version	NN
10_1101-436634	667	17	posted	post	VBN
10_1101-436634	667	18	January	January	NNP
10_1101-436634	667	19	5	5	CD
10_1101-436634	667	20	,	,	,
10_1101-436634	667	21	2021	2021	CD
10_1101-436634	667	22	.	.	.
10_1101-436634	667	23	;	;	:
10_1101-436634	667	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	667	25	:	:	:
10_1101-436634	667	26	bioRxiv	biorxiv	VB
10_1101-436634	667	27	preprint	preprint	NN
10_1101-436634	667	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	667	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	667	30	26	26	CD
10_1101-436634	667	31	Figure	Figure	NNP
10_1101-436634	667	32	2	2	CD
10_1101-436634	667	33	.	.	.
10_1101-436634	668	1	Overview	overview	NN
10_1101-436634	668	2	of	of	IN
10_1101-436634	668	3	input	input	NN
10_1101-436634	668	4	data	datum	NNS
10_1101-436634	668	5	considered	consider	VBN
10_1101-436634	668	6	and	and	CC
10_1101-436634	668	7	significant	significant	JJ
10_1101-436634	668	8	events	event	NNS
10_1101-436634	668	9	identified	identify	VBN
10_1101-436634	668	10	by	by	IN
10_1101-436634	668	11	RegTools	regtool	NNS
10_1101-436634	668	12	for	for	IN
10_1101-436634	668	13	each	each	DT
10_1101-436634	668	14	tumor	tumor	NN
10_1101-436634	668	15	type	type	NN
10_1101-436634	668	16	.	.	.
10_1101-436634	669	1	A	a	LS
10_1101-436634	669	2	)	)	-RRB-
10_1101-436634	669	3	Summary	summary	NN
10_1101-436634	669	4	of	of	IN
10_1101-436634	669	5	initial	initial	JJ
10_1101-436634	669	6	variants	variant	NNS
10_1101-436634	669	7	considered	consider	VBN
10_1101-436634	669	8	for	for	IN
10_1101-436634	669	9	analysis	analysis	NN
10_1101-436634	669	10	by	by	IN
10_1101-436634	669	11	RegTools	regtool	NNS
10_1101-436634	669	12	per	per	IN
10_1101-436634	669	13	sample	sample	NN
10_1101-436634	669	14	per	per	IN
10_1101-436634	669	15	tumor	tumor	NN
10_1101-436634	669	16	cohort	cohort	NN
10_1101-436634	669	17	.	.	.
10_1101-436634	670	1	Each	each	DT
10_1101-436634	670	2	sample	sample	NN
10_1101-436634	670	3	’s	’s	POS
10_1101-436634	670	4	variant	variant	JJ
10_1101-436634	670	5	count	count	NN
10_1101-436634	670	6	is	be	VBZ
10_1101-436634	670	7	plotted	plot	VBN
10_1101-436634	670	8	and	and	CC
10_1101-436634	670	9	violin	violin	NN
10_1101-436634	670	10	plots	plot	NNS
10_1101-436634	670	11	are	be	VBP
10_1101-436634	670	12	overlaid	overlay	VBN
10_1101-436634	670	13	for	for	IN
10_1101-436634	670	14	each	each	DT
10_1101-436634	670	15	cohort	cohort	NN
10_1101-436634	670	16	.	.	.
10_1101-436634	671	1	B	B	NNP
10_1101-436634	671	2	)	)	-RRB-
10_1101-436634	671	3	Summary	Summary	NNP
10_1101-436634	671	4	unique	unique	JJ
10_1101-436634	671	5	exon	exon	NN
10_1101-436634	671	6	-	-	HYPH
10_1101-436634	671	7	exon	exon	NN
10_1101-436634	671	8	junction	junction	NN
10_1101-436634	671	9	observations	observation	NNS
10_1101-436634	671	10	for	for	IN
10_1101-436634	671	11	each	each	DT
10_1101-436634	671	12	sample	sample	NN
10_1101-436634	671	13	.	.	.
10_1101-436634	672	1	Each	each	DT
10_1101-436634	672	2	sample	sample	NN
10_1101-436634	672	3	’s	’s	POS
10_1101-436634	672	4	unique	unique	JJ
10_1101-436634	672	5	junction	junction	NN
10_1101-436634	672	6	count	count	NN
10_1101-436634	672	7	is	be	VBZ
10_1101-436634	672	8	plotted	plot	VBN
10_1101-436634	672	9	and	and	CC
10_1101-436634	672	10	violin	violin	NN
10_1101-436634	672	11	plots	plot	NNS
10_1101-436634	672	12	are	be	VBP
10_1101-436634	672	13	overlaid	overlay	VBN
10_1101-436634	672	14	for	for	IN
10_1101-436634	672	15	each	each	DT
10_1101-436634	672	16	cohort	cohort	NN
10_1101-436634	672	17	.	.	.
10_1101-436634	673	1	C	C	NNP
10_1101-436634	673	2	)	)	-RRB-
10_1101-436634	673	3	Summary	Summary	NNP
10_1101-436634	673	4	of	of	IN
10_1101-436634	673	5	significant	significant	JJ
10_1101-436634	673	6	junction	junction	NN
10_1101-436634	673	7	types	type	NNS
10_1101-436634	673	8	for	for	IN
10_1101-436634	673	9	each	each	DT
10_1101-436634	673	10	cohort	cohort	NN
10_1101-436634	673	11	across	across	IN
10_1101-436634	673	12	each	each	DT
10_1101-436634	673	13	of	of	IN
10_1101-436634	673	14	the	the	DT
10_1101-436634	673	15	variant	variant	JJ
10_1101-436634	673	16	window	window	NN
10_1101-436634	673	17	sizes	size	NNS
10_1101-436634	673	18	that	that	WDT
10_1101-436634	673	19	were	be	VBD
10_1101-436634	673	20	used	use	VBN
10_1101-436634	673	21	in	in	IN
10_1101-436634	673	22	this	this	DT
10_1101-436634	673	23	analysis	analysis	NN
10_1101-436634	673	24	.	.	.
10_1101-436634	674	1	.CC	.CC	NFP
10_1101-436634	674	2	-	-	:
10_1101-436634	674	3	BY	by	IN
10_1101-436634	674	4	-	-	HYPH
10_1101-436634	674	5	NC	NC	NNP
10_1101-436634	674	6	-	-	HYPH
10_1101-436634	674	7	ND	ND	NNP
10_1101-436634	674	8	4.0	4.0	CD
10_1101-436634	674	9	International	international	JJ
10_1101-436634	674	10	licensea	licensea	NNS
10_1101-436634	674	11	certified	certify	VBN
10_1101-436634	674	12	by	by	IN
10_1101-436634	674	13	peer	peer	NN
10_1101-436634	674	14	review	review	NN
10_1101-436634	674	15	)	)	-RRB-
10_1101-436634	674	16	is	be	VBZ
10_1101-436634	674	17	the	the	DT
10_1101-436634	674	18	author	author	NN
10_1101-436634	674	19	/	/	SYM
10_1101-436634	674	20	funder	funder	NN
10_1101-436634	674	21	,	,	,
10_1101-436634	674	22	who	who	WP
10_1101-436634	674	23	has	have	VBZ
10_1101-436634	674	24	granted	grant	VBN
10_1101-436634	674	25	bioRxiv	biorxiv	IN
10_1101-436634	674	26	a	a	DT
10_1101-436634	674	27	license	license	NN
10_1101-436634	674	28	to	to	TO
10_1101-436634	674	29	display	display	VB
10_1101-436634	674	30	the	the	DT
10_1101-436634	674	31	preprint	preprint	NN
10_1101-436634	674	32	in	in	IN
10_1101-436634	674	33	perpetuity	perpetuity	NN
10_1101-436634	674	34	.	.	.
10_1101-436634	675	1	It	-PRON-	PRP
10_1101-436634	675	2	is	be	VBZ
10_1101-436634	675	3	made	make	VBN
10_1101-436634	675	4	available	available	JJ
10_1101-436634	675	5	under	under	IN
10_1101-436634	675	6	The	the	DT
10_1101-436634	675	7	copyright	copyright	NN
10_1101-436634	675	8	holder	holder	NN
10_1101-436634	675	9	for	for	IN
10_1101-436634	675	10	this	this	DT
10_1101-436634	675	11	preprint	preprint	NN
10_1101-436634	675	12	(	(	-LRB-
10_1101-436634	675	13	which	which	WDT
10_1101-436634	675	14	was	be	VBD
10_1101-436634	675	15	notthis	notthis	DT
10_1101-436634	675	16	version	version	NN
10_1101-436634	675	17	posted	post	VBN
10_1101-436634	675	18	January	January	NNP
10_1101-436634	675	19	5	5	CD
10_1101-436634	675	20	,	,	,
10_1101-436634	675	21	2021	2021	CD
10_1101-436634	675	22	.	.	.
10_1101-436634	675	23	;	;	:
10_1101-436634	675	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	675	25	:	:	:
10_1101-436634	675	26	bioRxiv	biorxiv	VB
10_1101-436634	675	27	preprint	preprint	NN
10_1101-436634	675	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	675	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	CC
10_1101-436634	675	30	27	27	CD
10_1101-436634	675	31	Figure	figure	NN
10_1101-436634	675	32	3	3	CD
10_1101-436634	675	33	.	.	.
10_1101-436634	676	1	Splice	splice	NN
10_1101-436634	676	2	regulatory	regulatory	JJ
10_1101-436634	676	3	variants	variant	NNS
10_1101-436634	676	4	often	often	RB
10_1101-436634	676	5	lead	lead	VBP
10_1101-436634	676	6	to	to	IN
10_1101-436634	676	7	the	the	DT
10_1101-436634	676	8	expression	expression	NN
10_1101-436634	676	9	of	of	IN
10_1101-436634	676	10	multiple	multiple	JJ
10_1101-436634	676	11	alternative	alternative	JJ
10_1101-436634	676	12	junctions	junction	NNS
10_1101-436634	676	13	.	.	.
10_1101-436634	677	1	A	a	LS
10_1101-436634	677	2	)	)	-RRB-
10_1101-436634	677	3	A	a	DT
10_1101-436634	677	4	single	single	JJ
10_1101-436634	677	5	variant	variant	NN
10_1101-436634	677	6	can	can	MD
10_1101-436634	677	7	result	result	VB
10_1101-436634	677	8	in	in	IN
10_1101-436634	677	9	either	either	DT
10_1101-436634	677	10	one	one	CD
10_1101-436634	677	11	or	or	CC
10_1101-436634	677	12	more	more	JJR
10_1101-436634	677	13	than	than	IN
10_1101-436634	677	14	one	one	CD
10_1101-436634	677	15	alternatively	alternatively	RB
10_1101-436634	677	16	spliced	spliced	JJ
10_1101-436634	677	17	junctions	junction	NNS
10_1101-436634	677	18	.	.	.
10_1101-436634	678	1	Depicted	Depicted	NNP
10_1101-436634	678	2	is	be	VBZ
10_1101-436634	678	3	a	a	DT
10_1101-436634	678	4	variant	variant	JJ
10_1101-436634	678	5	resulting	resulting	NN
10_1101-436634	678	6	in	in	IN
10_1101-436634	678	7	a	a	DT
10_1101-436634	678	8	single	single	JJ
10_1101-436634	678	9	novel	novel	NN
10_1101-436634	678	10	transcript	transcript	NN
10_1101-436634	678	11	product	product	NN
10_1101-436634	678	12	(	(	-LRB-
10_1101-436634	678	13	purple	purple	NNP
10_1101-436634	678	14	)	)	-RRB-
10_1101-436634	678	15	,	,	,
10_1101-436634	678	16	a	a	DT
10_1101-436634	678	17	variant	variant	JJ
10_1101-436634	678	18	resulting	result	VBG
10_1101-436634	678	19	in	in	IN
10_1101-436634	678	20	two	two	CD
10_1101-436634	678	21	novel	novel	JJ
10_1101-436634	678	22	transcript	transcript	NN
10_1101-436634	678	23	products	product	NNS
10_1101-436634	678	24	that	that	IN
10_1101-436634	678	25	both	both	DT
10_1101-436634	678	26	use	use	VBP
10_1101-436634	678	27	alternate	alternate	JJ
10_1101-436634	678	28	donor	donor	NN
10_1101-436634	678	29	sites	site	NNS
10_1101-436634	678	30	(	(	-LRB-
10_1101-436634	678	31	yellow	yellow	NNP
10_1101-436634	678	32	)	)	-RRB-
10_1101-436634	678	33	,	,	,
10_1101-436634	678	34	and	and	CC
10_1101-436634	678	35	a	a	DT
10_1101-436634	678	36	variant	variant	JJ
10_1101-436634	678	37	resulting	result	VBG
10_1101-436634	678	38	in	in	IN
10_1101-436634	678	39	multiple	multiple	JJ
10_1101-436634	678	40	junctions	junction	NNS
10_1101-436634	678	41	of	of	IN
10_1101-436634	678	42	different	different	JJ
10_1101-436634	678	43	types	type	NNS
10_1101-436634	678	44	(	(	-LRB-
10_1101-436634	678	45	teal	teal	NN
10_1101-436634	678	46	)	)	-RRB-
10_1101-436634	678	47	.	.	.
10_1101-436634	679	1	B	b	NN
10_1101-436634	679	2	)	)	-RRB-
10_1101-436634	679	3	Stacked	stack	VBD
10_1101-436634	679	4	bar	bar	NN
10_1101-436634	679	5	graph	graph	NN
10_1101-436634	679	6	visualizing	visualizing	NN
10_1101-436634	679	7	how	how	WRB
10_1101-436634	679	8	often	often	RB
10_1101-436634	679	9	a	a	DT
10_1101-436634	679	10	.CC	.CC	:
10_1101-436634	679	11	-	-	HYPH
10_1101-436634	679	12	BY	by	IN
10_1101-436634	679	13	-	-	HYPH
10_1101-436634	679	14	NC	NC	NNP
10_1101-436634	679	15	-	-	HYPH
10_1101-436634	679	16	ND	ND	NNP
10_1101-436634	679	17	4.0	4.0	CD
10_1101-436634	679	18	International	international	JJ
10_1101-436634	679	19	licensea	licensea	NNS
10_1101-436634	679	20	certified	certify	VBN
10_1101-436634	679	21	by	by	IN
10_1101-436634	679	22	peer	peer	NN
10_1101-436634	679	23	review	review	NN
10_1101-436634	679	24	)	)	-RRB-
10_1101-436634	679	25	is	be	VBZ
10_1101-436634	679	26	the	the	DT
10_1101-436634	679	27	author	author	NN
10_1101-436634	679	28	/	/	SYM
10_1101-436634	679	29	funder	funder	NN
10_1101-436634	679	30	,	,	,
10_1101-436634	679	31	who	who	WP
10_1101-436634	679	32	has	have	VBZ
10_1101-436634	679	33	granted	grant	VBN
10_1101-436634	679	34	bioRxiv	biorxiv	IN
10_1101-436634	679	35	a	a	DT
10_1101-436634	679	36	license	license	NN
10_1101-436634	679	37	to	to	TO
10_1101-436634	679	38	display	display	VB
10_1101-436634	679	39	the	the	DT
10_1101-436634	679	40	preprint	preprint	NN
10_1101-436634	679	41	in	in	IN
10_1101-436634	679	42	perpetuity	perpetuity	NN
10_1101-436634	679	43	.	.	.
10_1101-436634	680	1	It	-PRON-	PRP
10_1101-436634	680	2	is	be	VBZ
10_1101-436634	680	3	made	make	VBN
10_1101-436634	680	4	available	available	JJ
10_1101-436634	680	5	under	under	IN
10_1101-436634	680	6	The	the	DT
10_1101-436634	680	7	copyright	copyright	NN
10_1101-436634	680	8	holder	holder	NN
10_1101-436634	680	9	for	for	IN
10_1101-436634	680	10	this	this	DT
10_1101-436634	680	11	preprint	preprint	NN
10_1101-436634	680	12	(	(	-LRB-
10_1101-436634	680	13	which	which	WDT
10_1101-436634	680	14	was	be	VBD
10_1101-436634	680	15	notthis	notthis	DT
10_1101-436634	680	16	version	version	NN
10_1101-436634	680	17	posted	post	VBN
10_1101-436634	680	18	January	January	NNP
10_1101-436634	680	19	5	5	CD
10_1101-436634	680	20	,	,	,
10_1101-436634	680	21	2021	2021	CD
10_1101-436634	680	22	.	.	.
10_1101-436634	680	23	;	;	:
10_1101-436634	680	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	680	25	:	:	:
10_1101-436634	680	26	bioRxiv	biorxiv	VB
10_1101-436634	680	27	preprint	preprint	NN
10_1101-436634	680	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	680	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	680	30	28	28	CD
10_1101-436634	680	31	variant	variant	JJ
10_1101-436634	680	32	leads	lead	NNS
10_1101-436634	680	33	to	to	IN
10_1101-436634	680	34	each	each	DT
10_1101-436634	680	35	of	of	IN
10_1101-436634	680	36	the	the	DT
10_1101-436634	680	37	categories	category	NNS
10_1101-436634	680	38	mentioned	mention	VBN
10_1101-436634	680	39	above	above	RB
10_1101-436634	680	40	across	across	IN
10_1101-436634	680	41	the	the	DT
10_1101-436634	680	42	four	four	CD
10_1101-436634	680	43	RegTools	RegTools	NNP
10_1101-436634	680	44	variant	variant	JJ
10_1101-436634	680	45	windows	window	NNS
10_1101-436634	680	46	used	use	VBN
10_1101-436634	680	47	.	.	.
10_1101-436634	681	1	This	this	DT
10_1101-436634	681	2	analysis	analysis	NN
10_1101-436634	681	3	is	be	VBZ
10_1101-436634	681	4	for	for	IN
10_1101-436634	681	5	all	all	DT
10_1101-436634	681	6	variants	variant	NNS
10_1101-436634	681	7	that	that	WDT
10_1101-436634	681	8	RegTools	RegTools	NNP
10_1101-436634	681	9	identified	identify	VBN
10_1101-436634	681	10	as	as	IN
10_1101-436634	681	11	significant	significant	JJ
10_1101-436634	681	12	.	.	.
10_1101-436634	682	1	C	C	NNP
10_1101-436634	682	2	)	)	-RRB-
10_1101-436634	682	3	Bar	bar	VB
10_1101-436634	682	4	chart	chart	NN
10_1101-436634	682	5	showing	show	VBG
10_1101-436634	682	6	how	how	WRB
10_1101-436634	682	7	often	often	RB
10_1101-436634	682	8	each	each	DT
10_1101-436634	682	9	of	of	IN
10_1101-436634	682	10	the	the	DT
10_1101-436634	682	11	described	describe	VBN
10_1101-436634	682	12	junction	junction	NN
10_1101-436634	682	13	combinations	combination	NNS
10_1101-436634	682	14	occurs	occur	VBZ
10_1101-436634	682	15	when	when	WRB
10_1101-436634	682	16	a	a	DT
10_1101-436634	682	17	single	single	JJ
10_1101-436634	682	18	variant	variant	JJ
10_1101-436634	682	19	results	result	NNS
10_1101-436634	682	20	in	in	IN
10_1101-436634	682	21	multiple	multiple	JJ
10_1101-436634	682	22	junction	junction	NN
10_1101-436634	682	23	types	type	NNS
10_1101-436634	682	24	across	across	IN
10_1101-436634	682	25	each	each	DT
10_1101-436634	682	26	of	of	IN
10_1101-436634	682	27	the	the	DT
10_1101-436634	682	28	RegTools	RegTools	NNP
10_1101-436634	682	29	splice	splice	NN
10_1101-436634	682	30	variant	variant	JJ
10_1101-436634	682	31	windows	window	NNS
10_1101-436634	682	32	used	use	VBD
10_1101-436634	682	33	.	.	.
10_1101-436634	683	1	.CC	.CC	NFP
10_1101-436634	683	2	-	-	:
10_1101-436634	683	3	BY	by	IN
10_1101-436634	683	4	-	-	HYPH
10_1101-436634	683	5	NC	NC	NNP
10_1101-436634	683	6	-	-	HYPH
10_1101-436634	683	7	ND	ND	NNP
10_1101-436634	683	8	4.0	4.0	CD
10_1101-436634	683	9	International	international	JJ
10_1101-436634	683	10	licensea	licensea	NNS
10_1101-436634	683	11	certified	certify	VBN
10_1101-436634	683	12	by	by	IN
10_1101-436634	683	13	peer	peer	NN
10_1101-436634	683	14	review	review	NN
10_1101-436634	683	15	)	)	-RRB-
10_1101-436634	683	16	is	be	VBZ
10_1101-436634	683	17	the	the	DT
10_1101-436634	683	18	author	author	NN
10_1101-436634	683	19	/	/	SYM
10_1101-436634	683	20	funder	funder	NN
10_1101-436634	683	21	,	,	,
10_1101-436634	683	22	who	who	WP
10_1101-436634	683	23	has	have	VBZ
10_1101-436634	683	24	granted	grant	VBN
10_1101-436634	683	25	bioRxiv	biorxiv	IN
10_1101-436634	683	26	a	a	DT
10_1101-436634	683	27	license	license	NN
10_1101-436634	683	28	to	to	TO
10_1101-436634	683	29	display	display	VB
10_1101-436634	683	30	the	the	DT
10_1101-436634	683	31	preprint	preprint	NN
10_1101-436634	683	32	in	in	IN
10_1101-436634	683	33	perpetuity	perpetuity	NN
10_1101-436634	683	34	.	.	.
10_1101-436634	684	1	It	-PRON-	PRP
10_1101-436634	684	2	is	be	VBZ
10_1101-436634	684	3	made	make	VBN
10_1101-436634	684	4	available	available	JJ
10_1101-436634	684	5	under	under	IN
10_1101-436634	684	6	The	the	DT
10_1101-436634	684	7	copyright	copyright	NN
10_1101-436634	684	8	holder	holder	NN
10_1101-436634	684	9	for	for	IN
10_1101-436634	684	10	this	this	DT
10_1101-436634	684	11	preprint	preprint	NN
10_1101-436634	684	12	(	(	-LRB-
10_1101-436634	684	13	which	which	WDT
10_1101-436634	684	14	was	be	VBD
10_1101-436634	684	15	notthis	notthis	DT
10_1101-436634	684	16	version	version	NN
10_1101-436634	684	17	posted	post	VBN
10_1101-436634	684	18	January	January	NNP
10_1101-436634	684	19	5	5	CD
10_1101-436634	684	20	,	,	,
10_1101-436634	684	21	2021	2021	CD
10_1101-436634	684	22	.	.	.
10_1101-436634	684	23	;	;	:
10_1101-436634	684	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	684	25	:	:	:
10_1101-436634	684	26	bioRxiv	biorxiv	VB
10_1101-436634	684	27	preprint	preprint	NN
10_1101-436634	684	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	684	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NFP
10_1101-436634	684	30	29	29	CD
10_1101-436634	684	31	Figure	figure	NN
10_1101-436634	684	32	4	4	CD
10_1101-436634	684	33	.	.	.
10_1101-436634	685	1	Comparison	Comparison	NNP
10_1101-436634	685	2	of	of	IN
10_1101-436634	685	3	RegTools	RegTools	NNP
10_1101-436634	685	4	with	with	IN
10_1101-436634	685	5	other	other	JJ
10_1101-436634	685	6	tools	tool	NNS
10_1101-436634	685	7	that	that	WDT
10_1101-436634	685	8	identify	identify	VBP
10_1101-436634	685	9	potential	potential	JJ
10_1101-436634	685	10	splice	splice	NN
10_1101-436634	685	11	altering	alter	VBG
10_1101-436634	685	12	variants	variant	NNS
10_1101-436634	685	13	.	.	.
10_1101-436634	686	1	A	a	LS
10_1101-436634	686	2	)	)	-RRB-
10_1101-436634	686	3	Conceptual	conceptual	JJ
10_1101-436634	686	4	diagram	diagram	NN
10_1101-436634	686	5	of	of	IN
10_1101-436634	686	6	contrasting	contrast	VBG
10_1101-436634	686	7	approaches	approach	NNS
10_1101-436634	686	8	used	use	VBN
10_1101-436634	686	9	to	to	TO
10_1101-436634	686	10	identify	identify	VB
10_1101-436634	686	11	splice	splice	NN
10_1101-436634	686	12	regulatory	regulatory	JJ
10_1101-436634	686	13	tools	tool	NNS
10_1101-436634	686	14	/	/	SYM
10_1101-436634	686	15	methods	method	NNS
10_1101-436634	686	16	.	.	.
10_1101-436634	687	1	A	a	DT
10_1101-436634	687	2	red	red	JJ
10_1101-436634	687	3	dot	dot	NN
10_1101-436634	687	4	indicates	indicate	VBZ
10_1101-436634	687	5	that	that	IN
10_1101-436634	687	6	the	the	DT
10_1101-436634	687	7	source	source	NN
10_1101-436634	687	8	only	only	RB
10_1101-436634	687	9	considers	consider	VBZ
10_1101-436634	687	10	genomic	genomic	JJ
10_1101-436634	687	11	data	datum	NNS
10_1101-436634	687	12	for	for	IN
10_1101-436634	687	13	making	make	VBG
10_1101-436634	687	14	its	-PRON-	PRP$
10_1101-436634	687	15	calls	call	NNS
10_1101-436634	687	16	,	,	,
10_1101-436634	687	17	as	as	IN
10_1101-436634	687	18	opposed	oppose	VBN
10_1101-436634	687	19	to	to	IN
10_1101-436634	687	20	a	a	DT
10_1101-436634	687	21	combination	combination	NN
10_1101-436634	687	22	of	of	IN
10_1101-436634	687	23	genomic	genomic	JJ
10_1101-436634	687	24	and	and	CC
10_1101-436634	687	25	transcriptomic	transcriptomic	JJ
10_1101-436634	687	26	data	datum	NNS
10_1101-436634	687	27	.	.	.
10_1101-436634	688	1	B	b	NN
10_1101-436634	688	2	)	)	-RRB-
10_1101-436634	688	3	UpSet	UpSet	NNP
10_1101-436634	688	4	plot	plot	NN
10_1101-436634	688	5	comparing	compare	VBG
10_1101-436634	688	6	splice	splice	NN
10_1101-436634	688	7	altering	alter	VBG
10_1101-436634	688	8	variants	variant	NNS
10_1101-436634	688	9	identified	identify	VBN
10_1101-436634	688	10	by	by	IN
10_1101-436634	688	11	RegTools	regtool	NNS
10_1101-436634	688	12	to	to	IN
10_1101-436634	688	13	those	those	DT
10_1101-436634	688	14	identified	identify	VBN
10_1101-436634	688	15	by	by	IN
10_1101-436634	688	16	other	other	JJ
10_1101-436634	688	17	splice	splice	NN
10_1101-436634	688	18	variant	variant	JJ
10_1101-436634	688	19	predictors	predictor	NNS
10_1101-436634	688	20	and	and	CC
10_1101-436634	688	21	annotators	annotator	NNS
10_1101-436634	688	22	.	.	.
10_1101-436634	689	1	Each	each	DT
10_1101-436634	689	2	tool	tool	NN
10_1101-436634	689	3	and	and	CC
10_1101-436634	689	4	their	-PRON-	PRP$
10_1101-436634	689	5	total	total	JJ
10_1101-436634	689	6	number	number	NN
10_1101-436634	689	7	of	of	IN
10_1101-436634	689	8	variant	variant	JJ
10_1101-436634	689	9	predictions	prediction	NNS
10_1101-436634	689	10	are	be	VBP
10_1101-436634	689	11	shown	show	VBN
10_1101-436634	689	12	on	on	IN
10_1101-436634	689	13	the	the	DT
10_1101-436634	689	14	left	left	JJ
10_1101-436634	689	15	side	side	NN
10_1101-436634	689	16	bar	bar	NN
10_1101-436634	689	17	graph	graph	NN
10_1101-436634	689	18	.	.	.
10_1101-436634	690	1	The	the	DT
10_1101-436634	690	2	numbers	number	NNS
10_1101-436634	690	3	of	of	IN
10_1101-436634	690	4	variants	variant	NNS
10_1101-436634	690	5	specific	specific	JJ
10_1101-436634	690	6	to	to	IN
10_1101-436634	690	7	each	each	DT
10_1101-436634	690	8	tool	tool	NN
10_1101-436634	690	9	or	or	CC
10_1101-436634	690	10	shared	share	VBN
10_1101-436634	690	11	between	between	IN
10_1101-436634	690	12	different	different	JJ
10_1101-436634	690	13	combinations	combination	NNS
10_1101-436634	690	14	of	of	IN
10_1101-436634	690	15	tools	tool	NNS
10_1101-436634	690	16	are	be	VBP
10_1101-436634	690	17	indicated	indicate	VBN
10_1101-436634	690	18	by	by	IN
10_1101-436634	690	19	the	the	DT
10_1101-436634	690	20	bar	bar	NN
10_1101-436634	690	21	graph	graph	NN
10_1101-436634	690	22	along	along	IN
10_1101-436634	690	23	the	the	DT
10_1101-436634	690	24	top	top	NN
10_1101-436634	690	25	and	and	CC
10_1101-436634	690	26	the	the	DT
10_1101-436634	690	27	individual	individual	JJ
10_1101-436634	690	28	or	or	CC
10_1101-436634	690	29	connected	connected	JJ
10_1101-436634	690	30	dots	dot	NNS
10_1101-436634	690	31	.	.	.
10_1101-436634	691	1	.CC	.CC	NFP
10_1101-436634	691	2	-	-	:
10_1101-436634	691	3	BY	by	IN
10_1101-436634	691	4	-	-	HYPH
10_1101-436634	691	5	NC	NC	NNP
10_1101-436634	691	6	-	-	HYPH
10_1101-436634	691	7	ND	ND	NNP
10_1101-436634	691	8	4.0	4.0	CD
10_1101-436634	691	9	International	international	JJ
10_1101-436634	691	10	licensea	licensea	NNS
10_1101-436634	691	11	certified	certify	VBN
10_1101-436634	691	12	by	by	IN
10_1101-436634	691	13	peer	peer	NN
10_1101-436634	691	14	review	review	NN
10_1101-436634	691	15	)	)	-RRB-
10_1101-436634	691	16	is	be	VBZ
10_1101-436634	691	17	the	the	DT
10_1101-436634	691	18	author	author	NN
10_1101-436634	691	19	/	/	SYM
10_1101-436634	691	20	funder	funder	NN
10_1101-436634	691	21	,	,	,
10_1101-436634	691	22	who	who	WP
10_1101-436634	691	23	has	have	VBZ
10_1101-436634	691	24	granted	grant	VBN
10_1101-436634	691	25	bioRxiv	biorxiv	IN
10_1101-436634	691	26	a	a	DT
10_1101-436634	691	27	license	license	NN
10_1101-436634	691	28	to	to	TO
10_1101-436634	691	29	display	display	VB
10_1101-436634	691	30	the	the	DT
10_1101-436634	691	31	preprint	preprint	NN
10_1101-436634	691	32	in	in	IN
10_1101-436634	691	33	perpetuity	perpetuity	NN
10_1101-436634	691	34	.	.	.
10_1101-436634	692	1	It	-PRON-	PRP
10_1101-436634	692	2	is	be	VBZ
10_1101-436634	692	3	made	make	VBN
10_1101-436634	692	4	available	available	JJ
10_1101-436634	692	5	under	under	IN
10_1101-436634	692	6	The	the	DT
10_1101-436634	692	7	copyright	copyright	NN
10_1101-436634	692	8	holder	holder	NN
10_1101-436634	692	9	for	for	IN
10_1101-436634	692	10	this	this	DT
10_1101-436634	692	11	preprint	preprint	NN
10_1101-436634	692	12	(	(	-LRB-
10_1101-436634	692	13	which	which	WDT
10_1101-436634	692	14	was	be	VBD
10_1101-436634	692	15	notthis	notthis	DT
10_1101-436634	692	16	version	version	NN
10_1101-436634	692	17	posted	post	VBN
10_1101-436634	692	18	January	January	NNP
10_1101-436634	692	19	5	5	CD
10_1101-436634	692	20	,	,	,
10_1101-436634	692	21	2021	2021	CD
10_1101-436634	692	22	.	.	.
10_1101-436634	692	23	;	;	:
10_1101-436634	692	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	692	25	:	:	:
10_1101-436634	692	26	bioRxiv	biorxiv	VB
10_1101-436634	692	27	preprint	preprint	NN
10_1101-436634	692	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	692	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	692	30	30	30	CD
10_1101-436634	692	31	Figure	figure	NN
10_1101-436634	692	32	5	5	CD
10_1101-436634	692	33	.	.	.
10_1101-436634	693	1	Pan	pan	JJ
10_1101-436634	693	2	-	-	JJ
10_1101-436634	693	3	cancer	cancer	JJ
10_1101-436634	693	4	analysis	analysis	NN
10_1101-436634	693	5	of	of	IN
10_1101-436634	693	6	cohorts	cohort	NNS
10_1101-436634	693	7	from	from	IN
10_1101-436634	693	8	TCGA	TCGA	NNP
10_1101-436634	693	9	and	and	CC
10_1101-436634	693	10	MGI	MGI	NNP
10_1101-436634	693	11	reveals	reveal	VBZ
10_1101-436634	693	12	genes	gene	NNS
10_1101-436634	693	13	recurrently	recurrently	RB
10_1101-436634	693	14	disrupted	disrupt	VBN
10_1101-436634	693	15	by	by	IN
10_1101-436634	693	16	variants	variant	NNS
10_1101-436634	693	17	which	which	WDT
10_1101-436634	693	18	cause	cause	VBP
10_1101-436634	693	19	non	non	JJ
10_1101-436634	693	20	-	-	JJ
10_1101-436634	693	21	canonical	canonical	JJ
10_1101-436634	693	22	splicing	splicing	NN
10_1101-436634	693	23	patterns	pattern	NNS
10_1101-436634	693	24	Results	Results	NNPS
10_1101-436634	693	25	of	of	IN
10_1101-436634	693	26	analysis	analysis	NN
10_1101-436634	693	27	for	for	IN
10_1101-436634	693	28	recurrently	recurrently	RB
10_1101-436634	693	29	disrupted	disrupt	VBN
10_1101-436634	693	30	genes	gene	NNS
10_1101-436634	693	31	in	in	IN
10_1101-436634	693	32	each	each	DT
10_1101-436634	693	33	cohort	cohort	NN
10_1101-436634	693	34	.	.	.
10_1101-436634	694	1	Columns	column	NNS
10_1101-436634	694	2	correspond	correspond	VBP
10_1101-436634	694	3	to	to	IN
10_1101-436634	694	4	the	the	DT
10_1101-436634	694	5	20	20	CD
10_1101-436634	694	6	most	most	RBS
10_1101-436634	694	7	frequently	frequently	RB
10_1101-436634	694	8	recurring	recur	VBG
10_1101-436634	694	9	genes	gene	NNS
10_1101-436634	694	10	,	,	,
10_1101-436634	694	11	as	as	IN
10_1101-436634	694	12	ranked	rank	VBN
10_1101-436634	694	13	by	by	IN
10_1101-436634	694	14	fraction	fraction	NN
10_1101-436634	694	15	of	of	IN
10_1101-436634	694	16	samples	sample	NNS
10_1101-436634	694	17	.	.	.
10_1101-436634	695	1	Genes	gene	NNS
10_1101-436634	695	2	are	be	VBP
10_1101-436634	695	3	clustered	cluster	VBN
10_1101-436634	695	4	by	by	IN
10_1101-436634	695	5	whether	whether	IN
10_1101-436634	695	6	they	-PRON-	PRP
10_1101-436634	695	7	were	be	VBD
10_1101-436634	695	8	annotated	annotate	VBN
10_1101-436634	695	9	by	by	IN
10_1101-436634	695	10	the	the	DT
10_1101-436634	695	11	CGC	CGC	NNP
10_1101-436634	695	12	as	as	IN
10_1101-436634	695	13	an	an	DT
10_1101-436634	695	14	oncogene	oncogene	NN
10_1101-436634	695	15	(	(	-LRB-
10_1101-436634	695	16	red	red	NNP
10_1101-436634	695	17	)	)	-RRB-
10_1101-436634	695	18	,	,	,
10_1101-436634	695	19	an	an	DT
10_1101-436634	695	20	oncogene	oncogene	NN
10_1101-436634	695	21	and	and	CC
10_1101-436634	695	22	tumor	tumor	NN
10_1101-436634	695	23	suppressor	suppressor	NN
10_1101-436634	695	24	gene	gene	NN
10_1101-436634	695	25	(	(	-LRB-
10_1101-436634	695	26	yellow	yellow	NNP
10_1101-436634	695	27	)	)	-RRB-
10_1101-436634	695	28	,	,	,
10_1101-436634	695	29	a	a	DT
10_1101-436634	695	30	tumor	tumor	NN
10_1101-436634	695	31	suppressor	suppressor	NN
10_1101-436634	695	32	gene	gene	NN
10_1101-436634	695	33	(	(	-LRB-
10_1101-436634	695	34	green	green	NNP
10_1101-436634	695	35	)	)	-RRB-
10_1101-436634	695	36	,	,	,
10_1101-436634	695	37	or	or	CC
10_1101-436634	695	38	.CC	.CC	NFP
10_1101-436634	695	39	-	-	HYPH
10_1101-436634	695	40	BY	by	IN
10_1101-436634	695	41	-	-	HYPH
10_1101-436634	695	42	NC	NC	NNP
10_1101-436634	695	43	-	-	HYPH
10_1101-436634	695	44	ND	ND	NNP
10_1101-436634	695	45	4.0	4.0	CD
10_1101-436634	695	46	International	international	JJ
10_1101-436634	695	47	licensea	licensea	NNS
10_1101-436634	695	48	certified	certify	VBN
10_1101-436634	695	49	by	by	IN
10_1101-436634	695	50	peer	peer	NN
10_1101-436634	695	51	review	review	NN
10_1101-436634	695	52	)	)	-RRB-
10_1101-436634	695	53	is	be	VBZ
10_1101-436634	695	54	the	the	DT
10_1101-436634	695	55	author	author	NN
10_1101-436634	695	56	/	/	SYM
10_1101-436634	695	57	funder	funder	NN
10_1101-436634	695	58	,	,	,
10_1101-436634	695	59	who	who	WP
10_1101-436634	695	60	has	have	VBZ
10_1101-436634	695	61	granted	grant	VBN
10_1101-436634	695	62	bioRxiv	biorxiv	IN
10_1101-436634	695	63	a	a	DT
10_1101-436634	695	64	license	license	NN
10_1101-436634	695	65	to	to	TO
10_1101-436634	695	66	display	display	VB
10_1101-436634	695	67	the	the	DT
10_1101-436634	695	68	preprint	preprint	NN
10_1101-436634	695	69	in	in	IN
10_1101-436634	695	70	perpetuity	perpetuity	NN
10_1101-436634	695	71	.	.	.
10_1101-436634	696	1	It	-PRON-	PRP
10_1101-436634	696	2	is	be	VBZ
10_1101-436634	696	3	made	make	VBN
10_1101-436634	696	4	available	available	JJ
10_1101-436634	696	5	under	under	IN
10_1101-436634	696	6	The	the	DT
10_1101-436634	696	7	copyright	copyright	NN
10_1101-436634	696	8	holder	holder	NN
10_1101-436634	696	9	for	for	IN
10_1101-436634	696	10	this	this	DT
10_1101-436634	696	11	preprint	preprint	NN
10_1101-436634	696	12	(	(	-LRB-
10_1101-436634	696	13	which	which	WDT
10_1101-436634	696	14	was	be	VBD
10_1101-436634	696	15	notthis	notthis	DT
10_1101-436634	696	16	version	version	NN
10_1101-436634	696	17	posted	post	VBN
10_1101-436634	696	18	January	January	NNP
10_1101-436634	696	19	5	5	CD
10_1101-436634	696	20	,	,	,
10_1101-436634	696	21	2021	2021	CD
10_1101-436634	696	22	.	.	.
10_1101-436634	696	23	;	;	:
10_1101-436634	696	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	696	25	:	:	:
10_1101-436634	696	26	bioRxiv	biorxiv	VB
10_1101-436634	696	27	preprint	preprint	NN
10_1101-436634	696	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	696	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NNP
10_1101-436634	696	30	31	31	CD
10_1101-436634	696	31	another	another	DT
10_1101-436634	696	32	type	type	NN
10_1101-436634	696	33	of	of	IN
10_1101-436634	696	34	cancer	cancer	NN
10_1101-436634	696	35	-	-	HYPH
10_1101-436634	696	36	relevant	relevant	JJ
10_1101-436634	696	37	gene	gene	NN
10_1101-436634	696	38	.	.	.
10_1101-436634	697	1	Shading	shade	VBG
10_1101-436634	697	2	corresponds	correspond	NNS
10_1101-436634	697	3	to	to	IN
10_1101-436634	697	4	−log10(p	−log10(p	ADD
10_1101-436634	697	5	value	value	NN
10_1101-436634	697	6	)	)	-RRB-
10_1101-436634	697	7	and	and	CC
10_1101-436634	697	8	columns	column	NNS
10_1101-436634	697	9	represent	represent	VBP
10_1101-436634	697	10	cancer	cancer	NN
10_1101-436634	697	11	types	type	NNS
10_1101-436634	697	12	.	.	.
10_1101-436634	698	1	Red	red	JJ
10_1101-436634	698	2	marks	mark	NNS
10_1101-436634	698	3	within	within	IN
10_1101-436634	698	4	cells	cell	NNS
10_1101-436634	698	5	indicate	indicate	VBP
10_1101-436634	698	6	that	that	IN
10_1101-436634	698	7	the	the	DT
10_1101-436634	698	8	gene	gene	NN
10_1101-436634	698	9	was	be	VBD
10_1101-436634	698	10	annotated	annotate	VBN
10_1101-436634	698	11	by	by	IN
10_1101-436634	698	12	CHASMplus	CHASMplus	NNP
10_1101-436634	698	13	as	as	IN
10_1101-436634	698	14	a	a	DT
10_1101-436634	698	15	driver	driver	NN
10_1101-436634	698	16	within	within	IN
10_1101-436634	698	17	a	a	DT
10_1101-436634	698	18	given	give	VBN
10_1101-436634	698	19	TCGA	tcga	NN
10_1101-436634	698	20	cohort	cohort	NN
10_1101-436634	698	21	.	.	.
10_1101-436634	699	1	.CC	.CC	NFP
10_1101-436634	699	2	-	-	:
10_1101-436634	699	3	BY	by	IN
10_1101-436634	699	4	-	-	HYPH
10_1101-436634	699	5	NC	NC	NNP
10_1101-436634	699	6	-	-	HYPH
10_1101-436634	699	7	ND	ND	NNP
10_1101-436634	699	8	4.0	4.0	CD
10_1101-436634	699	9	International	international	JJ
10_1101-436634	699	10	licensea	licensea	NNS
10_1101-436634	699	11	certified	certify	VBN
10_1101-436634	699	12	by	by	IN
10_1101-436634	699	13	peer	peer	NN
10_1101-436634	699	14	review	review	NN
10_1101-436634	699	15	)	)	-RRB-
10_1101-436634	699	16	is	be	VBZ
10_1101-436634	699	17	the	the	DT
10_1101-436634	699	18	author	author	NN
10_1101-436634	699	19	/	/	SYM
10_1101-436634	699	20	funder	funder	NN
10_1101-436634	699	21	,	,	,
10_1101-436634	699	22	who	who	WP
10_1101-436634	699	23	has	have	VBZ
10_1101-436634	699	24	granted	grant	VBN
10_1101-436634	699	25	bioRxiv	biorxiv	IN
10_1101-436634	699	26	a	a	DT
10_1101-436634	699	27	license	license	NN
10_1101-436634	699	28	to	to	TO
10_1101-436634	699	29	display	display	VB
10_1101-436634	699	30	the	the	DT
10_1101-436634	699	31	preprint	preprint	NN
10_1101-436634	699	32	in	in	IN
10_1101-436634	699	33	perpetuity	perpetuity	NN
10_1101-436634	699	34	.	.	.
10_1101-436634	700	1	It	-PRON-	PRP
10_1101-436634	700	2	is	be	VBZ
10_1101-436634	700	3	made	make	VBN
10_1101-436634	700	4	available	available	JJ
10_1101-436634	700	5	under	under	IN
10_1101-436634	700	6	The	the	DT
10_1101-436634	700	7	copyright	copyright	NN
10_1101-436634	700	8	holder	holder	NN
10_1101-436634	700	9	for	for	IN
10_1101-436634	700	10	this	this	DT
10_1101-436634	700	11	preprint	preprint	NN
10_1101-436634	700	12	(	(	-LRB-
10_1101-436634	700	13	which	which	WDT
10_1101-436634	700	14	was	be	VBD
10_1101-436634	700	15	notthis	notthis	DT
10_1101-436634	700	16	version	version	NN
10_1101-436634	700	17	posted	post	VBN
10_1101-436634	700	18	January	January	NNP
10_1101-436634	700	19	5	5	CD
10_1101-436634	700	20	,	,	,
10_1101-436634	700	21	2021	2021	CD
10_1101-436634	700	22	.	.	.
10_1101-436634	700	23	;	;	:
10_1101-436634	700	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	700	25	:	:	:
10_1101-436634	700	26	bioRxiv	biorxiv	VB
10_1101-436634	700	27	preprint	preprint	NN
10_1101-436634	700	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	700	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	CD
10_1101-436634	700	30	32	32	CD
10_1101-436634	700	31	.CC	.CC	NFP
10_1101-436634	700	32	-	-	HYPH
10_1101-436634	700	33	BY	by	IN
10_1101-436634	700	34	-	-	HYPH
10_1101-436634	700	35	NC	NC	NNP
10_1101-436634	700	36	-	-	HYPH
10_1101-436634	700	37	ND	ND	NNP
10_1101-436634	700	38	4.0	4.0	CD
10_1101-436634	700	39	International	international	JJ
10_1101-436634	700	40	licensea	licensea	NNS
10_1101-436634	700	41	certified	certify	VBN
10_1101-436634	700	42	by	by	IN
10_1101-436634	700	43	peer	peer	NN
10_1101-436634	700	44	review	review	NN
10_1101-436634	700	45	)	)	-RRB-
10_1101-436634	700	46	is	be	VBZ
10_1101-436634	700	47	the	the	DT
10_1101-436634	700	48	author	author	NN
10_1101-436634	700	49	/	/	SYM
10_1101-436634	700	50	funder	funder	NN
10_1101-436634	700	51	,	,	,
10_1101-436634	700	52	who	who	WP
10_1101-436634	700	53	has	have	VBZ
10_1101-436634	700	54	granted	grant	VBN
10_1101-436634	700	55	bioRxiv	biorxiv	IN
10_1101-436634	700	56	a	a	DT
10_1101-436634	700	57	license	license	NN
10_1101-436634	700	58	to	to	TO
10_1101-436634	700	59	display	display	VB
10_1101-436634	700	60	the	the	DT
10_1101-436634	700	61	preprint	preprint	NN
10_1101-436634	700	62	in	in	IN
10_1101-436634	700	63	perpetuity	perpetuity	NN
10_1101-436634	700	64	.	.	.
10_1101-436634	701	1	It	-PRON-	PRP
10_1101-436634	701	2	is	be	VBZ
10_1101-436634	701	3	made	make	VBN
10_1101-436634	701	4	available	available	JJ
10_1101-436634	701	5	under	under	IN
10_1101-436634	701	6	The	the	DT
10_1101-436634	701	7	copyright	copyright	NN
10_1101-436634	701	8	holder	holder	NN
10_1101-436634	701	9	for	for	IN
10_1101-436634	701	10	this	this	DT
10_1101-436634	701	11	preprint	preprint	NN
10_1101-436634	701	12	(	(	-LRB-
10_1101-436634	701	13	which	which	WDT
10_1101-436634	701	14	was	be	VBD
10_1101-436634	701	15	notthis	notthis	DT
10_1101-436634	701	16	version	version	NN
10_1101-436634	701	17	posted	post	VBN
10_1101-436634	701	18	January	January	NNP
10_1101-436634	701	19	5	5	CD
10_1101-436634	701	20	,	,	,
10_1101-436634	701	21	2021	2021	CD
10_1101-436634	701	22	.	.	.
10_1101-436634	701	23	;	;	:
10_1101-436634	701	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	701	25	:	:	:
10_1101-436634	701	26	bioRxiv	biorxiv	VB
10_1101-436634	701	27	preprint	preprint	NN
10_1101-436634	701	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	701	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NFP
10_1101-436634	701	30	33	33	CD
10_1101-436634	701	31	Figure	figure	NN
10_1101-436634	701	32	6	6	CD
10_1101-436634	701	33	.	.	.
10_1101-436634	702	1	Several	several	JJ
10_1101-436634	702	2	SNVs	SNVs	NNPS
10_1101-436634	702	3	in	in	IN
10_1101-436634	702	4	B2	B2	NNP
10_1101-436634	702	5	M	M	NNP
10_1101-436634	702	6	associated	associate	VBN
10_1101-436634	702	7	with	with	IN
10_1101-436634	702	8	alternate	alternate	JJ
10_1101-436634	702	9	acceptor	acceptor	NN
10_1101-436634	702	10	and	and	CC
10_1101-436634	702	11	alternate	alternate	JJ
10_1101-436634	702	12	donor	donor	NN
10_1101-436634	702	13	usage	usage	NN
10_1101-436634	702	14	.	.	.
10_1101-436634	703	1	A	a	LS
10_1101-436634	703	2	)	)	-RRB-
10_1101-436634	703	3	IGV	igv	NN
10_1101-436634	703	4	snapshot	snapshot	NN
10_1101-436634	703	5	of	of	IN
10_1101-436634	703	6	three	three	CD
10_1101-436634	703	7	intronic	intronic	JJ
10_1101-436634	703	8	variant	variant	JJ
10_1101-436634	703	9	positions	position	NNS
10_1101-436634	703	10	found	find	VBD
10_1101-436634	703	11	to	to	TO
10_1101-436634	703	12	be	be	VB
10_1101-436634	703	13	associated	associate	VBN
10_1101-436634	703	14	with	with	IN
10_1101-436634	703	15	usage	usage	NN
10_1101-436634	703	16	of	of	IN
10_1101-436634	703	17	an	an	DT
10_1101-436634	703	18	alternate	alternate	JJ
10_1101-436634	703	19	acceptor	acceptor	NN
10_1101-436634	703	20	and	and	CC
10_1101-436634	703	21	alternative	alternative	JJ
10_1101-436634	703	22	donor	donor	NN
10_1101-436634	703	23	site	site	NN
10_1101-436634	703	24	that	that	WDT
10_1101-436634	703	25	leads	lead	VBZ
10_1101-436634	703	26	to	to	IN
10_1101-436634	703	27	formation	formation	NN
10_1101-436634	703	28	of	of	IN
10_1101-436634	703	29	novel	novel	JJ
10_1101-436634	703	30	transcript	transcript	NN
10_1101-436634	703	31	products	product	NNS
10_1101-436634	703	32	.	.	.
10_1101-436634	704	1	This	this	DT
10_1101-436634	704	2	result	result	NN
10_1101-436634	704	3	was	be	VBD
10_1101-436634	704	4	found	find	VBN
10_1101-436634	704	5	using	use	VBG
10_1101-436634	704	6	the	the	DT
10_1101-436634	704	7	default	default	NN
10_1101-436634	704	8	splice	splice	NN
10_1101-436634	704	9	variant	variant	JJ
10_1101-436634	704	10	window	window	NN
10_1101-436634	704	11	parameter	parameter	NN
10_1101-436634	704	12	(	(	-LRB-
10_1101-436634	704	13	i2e3	i2e3	ADD
10_1101-436634	704	14	)	)	-RRB-
10_1101-436634	704	15	.	.	.
10_1101-436634	705	1	B	b	NN
10_1101-436634	705	2	)	)	-RRB-
10_1101-436634	705	3	Zoomed	Zoomed	NNP
10_1101-436634	705	4	in	in	IN
10_1101-436634	705	5	view	view	NN
10_1101-436634	705	6	of	of	IN
10_1101-436634	705	7	the	the	DT
10_1101-436634	705	8	variants	variant	NNS
10_1101-436634	705	9	identified	identify	VBN
10_1101-436634	705	10	by	by	IN
10_1101-436634	705	11	RegTools	regtool	NNS
10_1101-436634	705	12	that	that	WDT
10_1101-436634	705	13	are	be	VBP
10_1101-436634	705	14	associated	associate	VBN
10_1101-436634	705	15	with	with	IN
10_1101-436634	705	16	alternate	alternate	JJ
10_1101-436634	705	17	acceptor	acceptor	NN
10_1101-436634	705	18	and	and	CC
10_1101-436634	705	19	donor	donor	NN
10_1101-436634	705	20	usage	usage	NN
10_1101-436634	705	21	.	.	.
10_1101-436634	706	1	Two	two	CD
10_1101-436634	706	2	of	of	IN
10_1101-436634	706	3	these	these	DT
10_1101-436634	706	4	variant	variant	JJ
10_1101-436634	706	5	positions	position	NNS
10_1101-436634	706	6	flank	flank	VBP
10_1101-436634	706	7	the	the	DT
10_1101-436634	706	8	acceptor	acceptor	NN
10_1101-436634	706	9	site	site	NN
10_1101-436634	706	10	and	and	CC
10_1101-436634	706	11	one	one	NN
10_1101-436634	706	12	flanks	flank	VBZ
10_1101-436634	706	13	the	the	DT
10_1101-436634	706	14	donor	donor	NN
10_1101-436634	706	15	site	site	NN
10_1101-436634	706	16	that	that	WDT
10_1101-436634	706	17	are	be	VBP
10_1101-436634	706	18	being	be	VBG
10_1101-436634	706	19	affected	affect	VBN
10_1101-436634	706	20	.	.	.
10_1101-436634	707	1	C	C	NNP
10_1101-436634	707	2	)	)	-RRB-
10_1101-436634	707	3	Sashimi	Sashimi	NNP
10_1101-436634	707	4	plot	plot	NN
10_1101-436634	707	5	visualizations	visualization	NNS
10_1101-436634	707	6	for	for	IN
10_1101-436634	707	7	samples	sample	NNS
10_1101-436634	707	8	containing	contain	VBG
10_1101-436634	707	9	the	the	DT
10_1101-436634	707	10	identified	identify	VBN
10_1101-436634	707	11	variants	variant	NNS
10_1101-436634	707	12	that	that	WDT
10_1101-436634	707	13	show	show	VBP
10_1101-436634	707	14	alternate	alternate	JJ
10_1101-436634	707	15	acceptor	acceptor	NN
10_1101-436634	707	16	usage	usage	NN
10_1101-436634	707	17	(	(	-LRB-
10_1101-436634	707	18	red	red	NNP
10_1101-436634	707	19	)	)	-RRB-
10_1101-436634	707	20	or	or	CC
10_1101-436634	707	21	alternate	alternate	JJ
10_1101-436634	707	22	donor	donor	NN
10_1101-436634	707	23	usage	usage	NN
10_1101-436634	707	24	(	(	-LRB-
10_1101-436634	707	25	orange	orange	NNP
10_1101-436634	707	26	)	)	-RRB-
10_1101-436634	707	27	.	.	.
10_1101-436634	708	1	.CC	.CC	NFP
10_1101-436634	708	2	-	-	:
10_1101-436634	708	3	BY	by	IN
10_1101-436634	708	4	-	-	HYPH
10_1101-436634	708	5	NC	NC	NNP
10_1101-436634	708	6	-	-	HYPH
10_1101-436634	708	7	ND	ND	NNP
10_1101-436634	708	8	4.0	4.0	CD
10_1101-436634	708	9	International	international	JJ
10_1101-436634	708	10	licensea	licensea	NNS
10_1101-436634	708	11	certified	certify	VBN
10_1101-436634	708	12	by	by	IN
10_1101-436634	708	13	peer	peer	NN
10_1101-436634	708	14	review	review	NN
10_1101-436634	708	15	)	)	-RRB-
10_1101-436634	708	16	is	be	VBZ
10_1101-436634	708	17	the	the	DT
10_1101-436634	708	18	author	author	NN
10_1101-436634	708	19	/	/	SYM
10_1101-436634	708	20	funder	funder	NN
10_1101-436634	708	21	,	,	,
10_1101-436634	708	22	who	who	WP
10_1101-436634	708	23	has	have	VBZ
10_1101-436634	708	24	granted	grant	VBN
10_1101-436634	708	25	bioRxiv	biorxiv	IN
10_1101-436634	708	26	a	a	DT
10_1101-436634	708	27	license	license	NN
10_1101-436634	708	28	to	to	TO
10_1101-436634	708	29	display	display	VB
10_1101-436634	708	30	the	the	DT
10_1101-436634	708	31	preprint	preprint	NN
10_1101-436634	708	32	in	in	IN
10_1101-436634	708	33	perpetuity	perpetuity	NN
10_1101-436634	708	34	.	.	.
10_1101-436634	709	1	It	-PRON-	PRP
10_1101-436634	709	2	is	be	VBZ
10_1101-436634	709	3	made	make	VBN
10_1101-436634	709	4	available	available	JJ
10_1101-436634	709	5	under	under	IN
10_1101-436634	709	6	The	the	DT
10_1101-436634	709	7	copyright	copyright	NN
10_1101-436634	709	8	holder	holder	NN
10_1101-436634	709	9	for	for	IN
10_1101-436634	709	10	this	this	DT
10_1101-436634	709	11	preprint	preprint	NN
10_1101-436634	709	12	(	(	-LRB-
10_1101-436634	709	13	which	which	WDT
10_1101-436634	709	14	was	be	VBD
10_1101-436634	709	15	notthis	notthis	DT
10_1101-436634	709	16	version	version	NN
10_1101-436634	709	17	posted	post	VBN
10_1101-436634	709	18	January	January	NNP
10_1101-436634	709	19	5	5	CD
10_1101-436634	709	20	,	,	,
10_1101-436634	709	21	2021	2021	CD
10_1101-436634	709	22	.	.	.
10_1101-436634	709	23	;	;	:
10_1101-436634	709	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	709	25	:	:	:
10_1101-436634	709	26	bioRxiv	biorxiv	VB
10_1101-436634	709	27	preprint	preprint	NN
10_1101-436634	709	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	709	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NFP
10_1101-436634	709	30	34	34	CD
10_1101-436634	709	31	Supplemental	Supplemental	NNP
10_1101-436634	709	32	Figures	Figures	NNPS
10_1101-436634	709	33	Supplementary	Supplementary	NNP
10_1101-436634	709	34	Figure	Figure	NNP
10_1101-436634	709	35	1	1	CD
10_1101-436634	709	36	.	.	.
10_1101-436634	710	1	Benchmarking	benchmarke	VBG
10_1101-436634	710	2	of	of	IN
10_1101-436634	710	3	each	each	DT
10_1101-436634	710	4	RegTools	RegTools	NNP
10_1101-436634	710	5	command	command	NN
10_1101-436634	710	6	.	.	.
10_1101-436634	711	1	The	the	DT
10_1101-436634	711	2	total	total	JJ
10_1101-436634	711	3	CPU	cpu	NN
10_1101-436634	711	4	time	time	NN
10_1101-436634	711	5	(	(	-LRB-
10_1101-436634	711	6	System	system	NN
10_1101-436634	711	7	Time	time	NN
10_1101-436634	711	8	+	+	CC
10_1101-436634	711	9	User	User	NNP
10_1101-436634	711	10	Time	Time	NNP
10_1101-436634	711	11	)	)	-RRB-
10_1101-436634	711	12	and	and	CC
10_1101-436634	711	13	real	real	JJ
10_1101-436634	711	14	time	time	NN
10_1101-436634	711	15	are	be	VBP
10_1101-436634	711	16	plotted	plot	VBN
10_1101-436634	711	17	against	against	IN
10_1101-436634	711	18	the	the	DT
10_1101-436634	711	19	number	number	NN
10_1101-436634	711	20	of	of	IN
10_1101-436634	711	21	entries	entry	NNS
10_1101-436634	711	22	processed	process	VBN
10_1101-436634	711	23	for	for	IN
10_1101-436634	711	24	each	each	DT
10_1101-436634	711	25	available	available	JJ
10_1101-436634	711	26	RegTools	RegTools	NNP
10_1101-436634	711	27	function	function	NN
10_1101-436634	711	28	using	use	VBG
10_1101-436634	711	29	10	10	CD
10_1101-436634	711	30	total	total	JJ
10_1101-436634	711	31	replicates	replicate	NNS
10_1101-436634	711	32	.	.	.
10_1101-436634	712	1	For	for	IN
10_1101-436634	712	2	the	the	DT
10_1101-436634	712	3	cis-	cis-	NN
10_1101-436634	712	4	splice	splice	NN
10_1101-436634	712	5	-	-	HYPH
10_1101-436634	712	6	effects	effect	NNS
10_1101-436634	712	7	identify	identify	VBP
10_1101-436634	712	8	/	/	SYM
10_1101-436634	712	9	cis	cis	NN
10_1101-436634	712	10	-	-	HYPH
10_1101-436634	712	11	splice	splice	NN
10_1101-436634	712	12	-	-	HYPH
10_1101-436634	712	13	effects	effect	NNS
10_1101-436634	712	14	associate	associate	NN
10_1101-436634	712	15	/	/	SYM
10_1101-436634	712	16	variants	variant	NNS
10_1101-436634	712	17	annotate	annotate	VBP
10_1101-436634	712	18	workflows	workflow	NNS
10_1101-436634	712	19	,	,	,
10_1101-436634	712	20	the	the	DT
10_1101-436634	712	21	number	number	NN
10_1101-436634	712	22	of	of	IN
10_1101-436634	712	23	entries	entry	NNS
10_1101-436634	712	24	corresponds	correspond	NNS
10_1101-436634	712	25	to	to	IN
10_1101-436634	712	26	the	the	DT
10_1101-436634	712	27	number	number	NN
10_1101-436634	712	28	of	of	IN
10_1101-436634	712	29	somatic	somatic	JJ
10_1101-436634	712	30	variants	variant	NNS
10_1101-436634	712	31	,	,	,
10_1101-436634	712	32	whereas	whereas	IN
10_1101-436634	712	33	the	the	DT
10_1101-436634	712	34	number	number	NN
10_1101-436634	712	35	of	of	IN
10_1101-436634	712	36	entries	entry	NNS
10_1101-436634	712	37	in	in	IN
10_1101-436634	712	38	the	the	DT
10_1101-436634	712	39	junctions	junction	NNS
10_1101-436634	712	40	extract	extract	NNP
10_1101-436634	712	41	/	/	SYM
10_1101-436634	712	42	junctions	junction	NNS
10_1101-436634	712	43	annotate	annotate	NN
10_1101-436634	712	44	/	/	SYM
10_1101-436634	712	45	compare_junctions	compare_junction	NNS
10_1101-436634	712	46	workflows	workflow	VBZ
10_1101-436634	712	47	corresponds	correspond	NNS
10_1101-436634	712	48	to	to	IN
10_1101-436634	712	49	the	the	DT
10_1101-436634	712	50	number	number	NN
10_1101-436634	712	51	of	of	IN
10_1101-436634	712	52	reads	read	NNS
10_1101-436634	712	53	processed	process	VBN
10_1101-436634	712	54	from	from	IN
10_1101-436634	712	55	a	a	DT
10_1101-436634	712	56	downsampled	downsampled	JJ
10_1101-436634	712	57	BAM	bam	NN
10_1101-436634	712	58	file	file	NN
10_1101-436634	712	59	,	,	,
10_1101-436634	712	60	the	the	DT
10_1101-436634	712	61	number	number	NN
10_1101-436634	712	62	of	of	IN
10_1101-436634	712	63	junctions	junction	NNS
10_1101-436634	712	64	processed	process	VBN
10_1101-436634	712	65	,	,	,
10_1101-436634	712	66	and	and	CC
10_1101-436634	712	67	the	the	DT
10_1101-436634	712	68	number	number	NN
10_1101-436634	712	69	of	of	IN
10_1101-436634	712	70	candidate	candidate	NN
10_1101-436634	712	71	variant	variant	JJ
10_1101-436634	712	72	junction	junction	NN
10_1101-436634	712	73	pairings	pairing	NNS
10_1101-436634	712	74	processed	process	VBN
10_1101-436634	712	75	,	,	,
10_1101-436634	712	76	respectively	respectively	RB
10_1101-436634	712	77	.	.	.
10_1101-436634	713	1	For	for	IN
10_1101-436634	713	2	compare_junctions	compare_junction	NNS
10_1101-436634	713	3	,	,	,
10_1101-436634	713	4	candidate	candidate	VBP
10_1101-436634	713	5	variant	variant	JJ
10_1101-436634	713	6	junction	junction	NN
10_1101-436634	713	7	pairings	pairing	NNS
10_1101-436634	713	8	were	be	VBD
10_1101-436634	713	9	compared	compare	VBN
10_1101-436634	713	10	across	across	IN
10_1101-436634	713	11	the	the	DT
10_1101-436634	713	12	number	number	NN
10_1101-436634	713	13	of	of	IN
10_1101-436634	713	14	samples	sample	NNS
10_1101-436634	713	15	in	in	IN
10_1101-436634	713	16	that	that	DT
10_1101-436634	713	17	cohort	cohort	NN
10_1101-436634	713	18	,	,	,
10_1101-436634	713	19	with	with	IN
10_1101-436634	713	20	the	the	DT
10_1101-436634	713	21	largest	large	JJS
10_1101-436634	713	22	being	be	VBG
10_1101-436634	713	23	1022	1022	CD
10_1101-436634	713	24	samples	sample	NNS
10_1101-436634	713	25	that	that	WDT
10_1101-436634	713	26	comprise	comprise	VBP
10_1101-436634	713	27	our	-PRON-	PRP$
10_1101-436634	713	28	BRCA	BRCA	NNP
10_1101-436634	713	29	cohort	cohort	NN
10_1101-436634	713	30	.	.	.
10_1101-436634	714	1	LOESS	LOESS	NNP
10_1101-436634	714	2	curves	curve	NNS
10_1101-436634	714	3	are	be	VBP
10_1101-436634	714	4	fitted	fit	VBN
10_1101-436634	714	5	onto	onto	IN
10_1101-436634	714	6	each	each	DT
10_1101-436634	714	7	plot	plot	NN
10_1101-436634	714	8	.	.	.
10_1101-436634	715	1	34	34	CD
10_1101-436634	715	2	of	of	IN
10_1101-436634	715	3	rt	rt	NNP
10_1101-436634	715	4	,	,	,
10_1101-436634	715	5	.CC	.CC	:
10_1101-436634	715	6	-	-	:
10_1101-436634	715	7	BY	by	IN
10_1101-436634	715	8	-	-	HYPH
10_1101-436634	715	9	NC	NC	NNP
10_1101-436634	715	10	-	-	HYPH
10_1101-436634	715	11	ND	ND	NNP
10_1101-436634	715	12	4.0	4.0	CD
10_1101-436634	715	13	International	international	JJ
10_1101-436634	715	14	licensea	licensea	NNS
10_1101-436634	715	15	certified	certify	VBN
10_1101-436634	715	16	by	by	IN
10_1101-436634	715	17	peer	peer	NN
10_1101-436634	715	18	review	review	NN
10_1101-436634	715	19	)	)	-RRB-
10_1101-436634	715	20	is	be	VBZ
10_1101-436634	715	21	the	the	DT
10_1101-436634	715	22	author	author	NN
10_1101-436634	715	23	/	/	SYM
10_1101-436634	715	24	funder	funder	NN
10_1101-436634	715	25	,	,	,
10_1101-436634	715	26	who	who	WP
10_1101-436634	715	27	has	have	VBZ
10_1101-436634	715	28	granted	grant	VBN
10_1101-436634	715	29	bioRxiv	biorxiv	IN
10_1101-436634	715	30	a	a	DT
10_1101-436634	715	31	license	license	NN
10_1101-436634	715	32	to	to	TO
10_1101-436634	715	33	display	display	VB
10_1101-436634	715	34	the	the	DT
10_1101-436634	715	35	preprint	preprint	NN
10_1101-436634	715	36	in	in	IN
10_1101-436634	715	37	perpetuity	perpetuity	NN
10_1101-436634	715	38	.	.	.
10_1101-436634	716	1	It	-PRON-	PRP
10_1101-436634	716	2	is	be	VBZ
10_1101-436634	716	3	made	make	VBN
10_1101-436634	716	4	available	available	JJ
10_1101-436634	716	5	under	under	IN
10_1101-436634	716	6	The	the	DT
10_1101-436634	716	7	copyright	copyright	NN
10_1101-436634	716	8	holder	holder	NN
10_1101-436634	716	9	for	for	IN
10_1101-436634	716	10	this	this	DT
10_1101-436634	716	11	preprint	preprint	NN
10_1101-436634	716	12	(	(	-LRB-
10_1101-436634	716	13	which	which	WDT
10_1101-436634	716	14	was	be	VBD
10_1101-436634	716	15	notthis	notthis	DT
10_1101-436634	716	16	version	version	NN
10_1101-436634	716	17	posted	post	VBN
10_1101-436634	716	18	January	January	NNP
10_1101-436634	716	19	5	5	CD
10_1101-436634	716	20	,	,	,
10_1101-436634	716	21	2021	2021	CD
10_1101-436634	716	22	.	.	.
10_1101-436634	716	23	;	;	:
10_1101-436634	716	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	716	25	:	:	:
10_1101-436634	716	26	bioRxiv	biorxiv	VB
10_1101-436634	716	27	preprint	preprint	NN
10_1101-436634	716	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	716	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NFP
10_1101-436634	716	30	35	35	CD
10_1101-436634	716	31	Supplementary	Supplementary	NNP
10_1101-436634	716	32	Figure	Figure	NNP
10_1101-436634	716	33	2	2	CD
10_1101-436634	716	34	.	.	.
10_1101-436634	717	1	Summary	summary	NN
10_1101-436634	717	2	of	of	IN
10_1101-436634	717	3	variants	variant	NNS
10_1101-436634	717	4	analyzed	analyze	VBN
10_1101-436634	717	5	by	by	IN
10_1101-436634	717	6	RegTools	regtool	NNS
10_1101-436634	717	7	in	in	IN
10_1101-436634	717	8	each	each	DT
10_1101-436634	717	9	tumor	tumor	NN
10_1101-436634	717	10	cohort	cohort	NN
10_1101-436634	717	11	Summary	Summary	NNP
10_1101-436634	717	12	of	of	IN
10_1101-436634	717	13	the	the	DT
10_1101-436634	717	14	starting	start	VBG
10_1101-436634	717	15	number	number	NN
10_1101-436634	717	16	of	of	IN
10_1101-436634	717	17	high	high	JJ
10_1101-436634	717	18	quality	quality	NN
10_1101-436634	717	19	variants	variant	NNS
10_1101-436634	717	20	per	per	IN
10_1101-436634	717	21	sample	sample	NN
10_1101-436634	717	22	,	,	,
10_1101-436634	717	23	the	the	DT
10_1101-436634	717	24	number	number	NN
10_1101-436634	717	25	of	of	IN
10_1101-436634	717	26	initial	initial	JJ
10_1101-436634	717	27	variants	variant	NNS
10_1101-436634	717	28	considered	consider	VBN
10_1101-436634	717	29	for	for	IN
10_1101-436634	717	30	analysis	analysis	NN
10_1101-436634	717	31	by	by	IN
10_1101-436634	717	32	RegTools	regtool	NNS
10_1101-436634	717	33	for	for	IN
10_1101-436634	717	34	each	each	DT
10_1101-436634	717	35	variant	variant	JJ
10_1101-436634	717	36	window	window	NN
10_1101-436634	717	37	used	use	VBN
10_1101-436634	717	38	per	per	IN
10_1101-436634	717	39	tumor	tumor	NN
10_1101-436634	717	40	cohort	cohort	NN
10_1101-436634	717	41	,	,	,
10_1101-436634	717	42	and	and	CC
10_1101-436634	717	43	the	the	DT
10_1101-436634	717	44	number	number	NN
10_1101-436634	717	45	of	of	IN
10_1101-436634	717	46	significant	significant	JJ
10_1101-436634	717	47	variants	variant	NNS
10_1101-436634	717	48	for	for	IN
10_1101-436634	717	49	each	each	DT
10_1101-436634	717	50	variant	variant	JJ
10_1101-436634	717	51	window	window	NN
10_1101-436634	717	52	used	use	VBN
10_1101-436634	717	53	per	per	IN
10_1101-436634	717	54	tumor	tumor	NN
10_1101-436634	717	55	cohort	cohort	NN
10_1101-436634	717	56	.	.	.
10_1101-436634	718	1	.CC	.CC	NFP
10_1101-436634	718	2	-	-	:
10_1101-436634	718	3	BY	by	IN
10_1101-436634	718	4	-	-	HYPH
10_1101-436634	718	5	NC	NC	NNP
10_1101-436634	718	6	-	-	HYPH
10_1101-436634	718	7	ND	ND	NNP
10_1101-436634	718	8	4.0	4.0	CD
10_1101-436634	718	9	International	international	JJ
10_1101-436634	718	10	licensea	licensea	NNS
10_1101-436634	718	11	certified	certify	VBN
10_1101-436634	718	12	by	by	IN
10_1101-436634	718	13	peer	peer	NN
10_1101-436634	718	14	review	review	NN
10_1101-436634	718	15	)	)	-RRB-
10_1101-436634	718	16	is	be	VBZ
10_1101-436634	718	17	the	the	DT
10_1101-436634	718	18	author	author	NN
10_1101-436634	718	19	/	/	SYM
10_1101-436634	718	20	funder	funder	NN
10_1101-436634	718	21	,	,	,
10_1101-436634	718	22	who	who	WP
10_1101-436634	718	23	has	have	VBZ
10_1101-436634	718	24	granted	grant	VBN
10_1101-436634	718	25	bioRxiv	biorxiv	IN
10_1101-436634	718	26	a	a	DT
10_1101-436634	718	27	license	license	NN
10_1101-436634	718	28	to	to	TO
10_1101-436634	718	29	display	display	VB
10_1101-436634	718	30	the	the	DT
10_1101-436634	718	31	preprint	preprint	NN
10_1101-436634	718	32	in	in	IN
10_1101-436634	718	33	perpetuity	perpetuity	NN
10_1101-436634	718	34	.	.	.
10_1101-436634	719	1	It	-PRON-	PRP
10_1101-436634	719	2	is	be	VBZ
10_1101-436634	719	3	made	make	VBN
10_1101-436634	719	4	available	available	JJ
10_1101-436634	719	5	under	under	IN
10_1101-436634	719	6	The	the	DT
10_1101-436634	719	7	copyright	copyright	NN
10_1101-436634	719	8	holder	holder	NN
10_1101-436634	719	9	for	for	IN
10_1101-436634	719	10	this	this	DT
10_1101-436634	719	11	preprint	preprint	NN
10_1101-436634	719	12	(	(	-LRB-
10_1101-436634	719	13	which	which	WDT
10_1101-436634	719	14	was	be	VBD
10_1101-436634	719	15	notthis	notthis	DT
10_1101-436634	719	16	version	version	NN
10_1101-436634	719	17	posted	post	VBN
10_1101-436634	719	18	January	January	NNP
10_1101-436634	719	19	5	5	CD
10_1101-436634	719	20	,	,	,
10_1101-436634	719	21	2021	2021	CD
10_1101-436634	719	22	.	.	.
10_1101-436634	719	23	;	;	:
10_1101-436634	719	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	719	25	:	:	:
10_1101-436634	719	26	bioRxiv	biorxiv	VB
10_1101-436634	719	27	preprint	preprint	NN
10_1101-436634	719	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	719	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	CC
10_1101-436634	719	30	36	36	CD
10_1101-436634	719	31	Supplementary	Supplementary	NNP
10_1101-436634	719	32	Figure	Figure	NNP
10_1101-436634	719	33	3	3	CD
10_1101-436634	719	34	.	.	.
10_1101-436634	720	1	Visualization	visualization	NN
10_1101-436634	720	2	of	of	IN
10_1101-436634	720	3	junctions	junction	NNS
10_1101-436634	720	4	across	across	IN
10_1101-436634	720	5	cohorts	cohort	NNS
10_1101-436634	720	6	.	.	.
10_1101-436634	721	1	Summary	summary	NN
10_1101-436634	721	2	of	of	IN
10_1101-436634	721	3	the	the	DT
10_1101-436634	721	4	total	total	JJ
10_1101-436634	721	5	junction	junction	NN
10_1101-436634	721	6	read	read	VBD
10_1101-436634	721	7	counts	count	NNS
10_1101-436634	721	8	,	,	,
10_1101-436634	721	9	unique	unique	JJ
10_1101-436634	721	10	junctions	junction	NNS
10_1101-436634	721	11	(	(	-LRB-
10_1101-436634	721	12	all	all	DT
10_1101-436634	721	13	types	type	NNS
10_1101-436634	721	14	)	)	-RRB-
10_1101-436634	721	15	,	,	,
10_1101-436634	721	16	unique	unique	JJ
10_1101-436634	721	17	known	know	VBN
10_1101-436634	721	18	(	(	-LRB-
10_1101-436634	721	19	DA	DA	NNP
10_1101-436634	721	20	)	)	-RRB-
10_1101-436634	721	21	junctions	junction	NNS
10_1101-436634	721	22	,	,	,
10_1101-436634	721	23	unique	unique	JJ
10_1101-436634	721	24	known	know	VBN
10_1101-436634	721	25	(	(	-LRB-
10_1101-436634	721	26	DA	DA	NNP
10_1101-436634	721	27	)	)	-RRB-
10_1101-436634	721	28	junctions	junction	NNS
10_1101-436634	721	29	not	not	RB
10_1101-436634	721	30	found	find	VBN
10_1101-436634	721	31	in	in	IN
10_1101-436634	721	32	GTEx	GTEx	NNS
10_1101-436634	721	33	,	,	,
10_1101-436634	721	34	unique	unique	JJ
10_1101-436634	721	35	D	d	NN
10_1101-436634	721	36	,	,	,
10_1101-436634	721	37	A	A	NNP
10_1101-436634	721	38	,	,	,
10_1101-436634	721	39	NDA	NDA	NNP
10_1101-436634	721	40	junctions	junction	NNS
10_1101-436634	721	41	,	,	,
10_1101-436634	721	42	and	and	CC
10_1101-436634	721	43	unique	unique	JJ
10_1101-436634	721	44	D	d	NN
10_1101-436634	721	45	,	,	,
10_1101-436634	721	46	A	A	NNP
10_1101-436634	721	47	,	,	,
10_1101-436634	721	48	NDA	NDA	NNP
10_1101-436634	721	49	junctions	junction	NNS
10_1101-436634	721	50	not	not	RB
10_1101-436634	721	51	found	find	VBN
10_1101-436634	721	52	in	in	IN
10_1101-436634	721	53	GTEx	GTEx	NNS
10_1101-436634	721	54	per	per	IN
10_1101-436634	721	55	sample	sample	NN
10_1101-436634	721	56	per	per	IN
10_1101-436634	721	57	cohort	cohort	NN
10_1101-436634	721	58	.	.	.
10_1101-436634	722	1	.CC	.CC	NFP
10_1101-436634	722	2	-	-	:
10_1101-436634	722	3	BY	by	IN
10_1101-436634	722	4	-	-	HYPH
10_1101-436634	722	5	NC	NC	NNP
10_1101-436634	722	6	-	-	HYPH
10_1101-436634	722	7	ND	ND	NNP
10_1101-436634	722	8	4.0	4.0	CD
10_1101-436634	722	9	International	international	JJ
10_1101-436634	722	10	licensea	licensea	NNS
10_1101-436634	722	11	certified	certify	VBN
10_1101-436634	722	12	by	by	IN
10_1101-436634	722	13	peer	peer	NN
10_1101-436634	722	14	review	review	NN
10_1101-436634	722	15	)	)	-RRB-
10_1101-436634	722	16	is	be	VBZ
10_1101-436634	722	17	the	the	DT
10_1101-436634	722	18	author	author	NN
10_1101-436634	722	19	/	/	SYM
10_1101-436634	722	20	funder	funder	NN
10_1101-436634	722	21	,	,	,
10_1101-436634	722	22	who	who	WP
10_1101-436634	722	23	has	have	VBZ
10_1101-436634	722	24	granted	grant	VBN
10_1101-436634	722	25	bioRxiv	biorxiv	IN
10_1101-436634	722	26	a	a	DT
10_1101-436634	722	27	license	license	NN
10_1101-436634	722	28	to	to	TO
10_1101-436634	722	29	display	display	VB
10_1101-436634	722	30	the	the	DT
10_1101-436634	722	31	preprint	preprint	NN
10_1101-436634	722	32	in	in	IN
10_1101-436634	722	33	perpetuity	perpetuity	NN
10_1101-436634	722	34	.	.	.
10_1101-436634	723	1	It	-PRON-	PRP
10_1101-436634	723	2	is	be	VBZ
10_1101-436634	723	3	made	make	VBN
10_1101-436634	723	4	available	available	JJ
10_1101-436634	723	5	under	under	IN
10_1101-436634	723	6	The	the	DT
10_1101-436634	723	7	copyright	copyright	NN
10_1101-436634	723	8	holder	holder	NN
10_1101-436634	723	9	for	for	IN
10_1101-436634	723	10	this	this	DT
10_1101-436634	723	11	preprint	preprint	NN
10_1101-436634	723	12	(	(	-LRB-
10_1101-436634	723	13	which	which	WDT
10_1101-436634	723	14	was	be	VBD
10_1101-436634	723	15	notthis	notthis	DT
10_1101-436634	723	16	version	version	NN
10_1101-436634	723	17	posted	post	VBN
10_1101-436634	723	18	January	January	NNP
10_1101-436634	723	19	5	5	CD
10_1101-436634	723	20	,	,	,
10_1101-436634	723	21	2021	2021	CD
10_1101-436634	723	22	.	.	.
10_1101-436634	723	23	;	;	:
10_1101-436634	723	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	723	25	:	:	:
10_1101-436634	723	26	bioRxiv	biorxiv	VB
10_1101-436634	723	27	preprint	preprint	NN
10_1101-436634	723	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	723	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	723	30	37	37	CD
10_1101-436634	723	31	Supplementary	Supplementary	NNP
10_1101-436634	723	32	Figure	Figure	NNP
10_1101-436634	723	33	4	4	CD
10_1101-436634	723	34	:	:	:
10_1101-436634	723	35	Intronic	intronic	JJ
10_1101-436634	723	36	SNV	SNV	NNP
10_1101-436634	723	37	in	in	IN
10_1101-436634	723	38	CTTN	CTTN	NNP
10_1101-436634	723	39	associated	associate	VBN
10_1101-436634	723	40	with	with	IN
10_1101-436634	723	41	an	an	DT
10_1101-436634	723	42	exon	exon	JJ
10_1101-436634	723	43	skipping	skipping	NN
10_1101-436634	723	44	event	event	NN
10_1101-436634	723	45	.	.	.
10_1101-436634	724	1	A	a	LS
10_1101-436634	724	2	)	)	-RRB-
10_1101-436634	724	3	IGV	igv	NN
10_1101-436634	724	4	snapshot	snapshot	NN
10_1101-436634	724	5	of	of	IN
10_1101-436634	724	6	a	a	DT
10_1101-436634	724	7	single	single	JJ
10_1101-436634	724	8	nucleotide	nucleotide	JJ
10_1101-436634	724	9	variant	variant	NN
10_1101-436634	724	10	(	(	-LRB-
10_1101-436634	724	11	GRCh38	grch38	NN
10_1101-436634	724	12	,	,	,
10_1101-436634	724	13	chr11	chr11	NN
10_1101-436634	724	14	:	:	:
10_1101-436634	724	15	g.70407517G	g.70407517g	ADD
10_1101-436634	724	16	>	>	XX
10_1101-436634	724	17	C	C	NNP
10_1101-436634	724	18	)	)	-RRB-
10_1101-436634	724	19	within	within	IN
10_1101-436634	724	20	an	an	DT
10_1101-436634	724	21	intron	intron	NN
10_1101-436634	724	22	of	of	IN
10_1101-436634	724	23	CTTN	CTTN	NNP
10_1101-436634	724	24	in	in	IN
10_1101-436634	724	25	LUAD	LUAD	NNP
10_1101-436634	724	26	sample	sample	NN
10_1101-436634	724	27	TCGA-86	TCGA-86	NNP
10_1101-436634	724	28	-	-	HYPH
10_1101-436634	724	29	6851	6851	CD
10_1101-436634	724	30	-	-	HYPH
10_1101-436634	724	31	01A.	01a.	CD
10_1101-436634	725	1	This	this	DT
10_1101-436634	725	2	variant	variant	NN
10_1101-436634	725	3	is	be	VBZ
10_1101-436634	725	4	associated	associate	VBN
10_1101-436634	725	5	with	with	IN
10_1101-436634	725	6	an	an	DT
10_1101-436634	725	7	exon	exon	JJ
10_1101-436634	725	8	skipping	skipping	NN
10_1101-436634	725	9	event	event	NN
10_1101-436634	725	10	causing	cause	VBG
10_1101-436634	725	11	the	the	DT
10_1101-436634	725	12	formation	formation	NN
10_1101-436634	725	13	of	of	IN
10_1101-436634	725	14	an	an	DT
10_1101-436634	725	15	NDA	NDA	NNP
10_1101-436634	725	16	junction	junction	NN
10_1101-436634	725	17	,	,	,
10_1101-436634	725	18	JUNC00027688	JUNC00027688	NNP
10_1101-436634	725	19	,	,	,
10_1101-436634	725	20	which	which	WDT
10_1101-436634	725	21	has	have	VBZ
10_1101-436634	725	22	44	44	CD
10_1101-436634	725	23	reads	read	NNS
10_1101-436634	725	24	of	of	IN
10_1101-436634	725	25	support	support	NN
10_1101-436634	725	26	.	.	.
10_1101-436634	726	1	The	the	DT
10_1101-436634	726	2	variant	variant	NN
10_1101-436634	726	3	was	be	VBD
10_1101-436634	726	4	identified	identify	VBN
10_1101-436634	726	5	by	by	IN
10_1101-436634	726	6	RegTools	RegTools	NNP
10_1101-436634	726	7	,	,	,
10_1101-436634	726	8	VEP	VEP	NNP
10_1101-436634	726	9	,	,	,
10_1101-436634	726	10	and	and	CC
10_1101-436634	726	11	Veridical	veridical	JJ
10_1101-436634	726	12	but	but	CC
10_1101-436634	726	13	no	no	DT
10_1101-436634	726	14	other	other	JJ
10_1101-436634	726	15	tools	tool	NNS
10_1101-436634	726	16	.	.	.
10_1101-436634	727	1	This	this	DT
10_1101-436634	727	2	result	result	NN
10_1101-436634	727	3	was	be	VBD
10_1101-436634	727	4	found	find	VBN
10_1101-436634	727	5	using	use	VBG
10_1101-436634	727	6	the	the	DT
10_1101-436634	727	7	default	default	NN
10_1101-436634	727	8	splice	splice	NN
10_1101-436634	727	9	variant	variant	JJ
10_1101-436634	727	10	window	window	NN
10_1101-436634	727	11	parameter	parameter	NN
10_1101-436634	727	12	(	(	-LRB-
10_1101-436634	727	13	i2e3	i2e3	ADD
10_1101-436634	727	14	)	)	-RRB-
10_1101-436634	727	15	.	.	.
10_1101-436634	728	1	B	b	NN
10_1101-436634	728	2	)	)	-RRB-
10_1101-436634	728	3	Sashimi	Sashimi	NNP
10_1101-436634	728	4	plot	plot	NN
10_1101-436634	728	5	visualization	visualization	NN
10_1101-436634	728	6	of	of	IN
10_1101-436634	728	7	the	the	DT
10_1101-436634	728	8	novel	novel	JJ
10_1101-436634	728	9	junction	junction	NN
10_1101-436634	728	10	.	.	.
10_1101-436634	729	1	.CC	.CC	NFP
10_1101-436634	729	2	-	-	:
10_1101-436634	729	3	BY	by	IN
10_1101-436634	729	4	-	-	HYPH
10_1101-436634	729	5	NC	NC	NNP
10_1101-436634	729	6	-	-	HYPH
10_1101-436634	729	7	ND	ND	NNP
10_1101-436634	729	8	4.0	4.0	CD
10_1101-436634	729	9	International	international	JJ
10_1101-436634	729	10	licensea	licensea	NNS
10_1101-436634	729	11	certified	certify	VBN
10_1101-436634	729	12	by	by	IN
10_1101-436634	729	13	peer	peer	NN
10_1101-436634	729	14	review	review	NN
10_1101-436634	729	15	)	)	-RRB-
10_1101-436634	729	16	is	be	VBZ
10_1101-436634	729	17	the	the	DT
10_1101-436634	729	18	author	author	NN
10_1101-436634	729	19	/	/	SYM
10_1101-436634	729	20	funder	funder	NN
10_1101-436634	729	21	,	,	,
10_1101-436634	729	22	who	who	WP
10_1101-436634	729	23	has	have	VBZ
10_1101-436634	729	24	granted	grant	VBN
10_1101-436634	729	25	bioRxiv	biorxiv	IN
10_1101-436634	729	26	a	a	DT
10_1101-436634	729	27	license	license	NN
10_1101-436634	729	28	to	to	TO
10_1101-436634	729	29	display	display	VB
10_1101-436634	729	30	the	the	DT
10_1101-436634	729	31	preprint	preprint	NN
10_1101-436634	729	32	in	in	IN
10_1101-436634	729	33	perpetuity	perpetuity	NN
10_1101-436634	729	34	.	.	.
10_1101-436634	730	1	It	-PRON-	PRP
10_1101-436634	730	2	is	be	VBZ
10_1101-436634	730	3	made	make	VBN
10_1101-436634	730	4	available	available	JJ
10_1101-436634	730	5	under	under	IN
10_1101-436634	730	6	The	the	DT
10_1101-436634	730	7	copyright	copyright	NN
10_1101-436634	730	8	holder	holder	NN
10_1101-436634	730	9	for	for	IN
10_1101-436634	730	10	this	this	DT
10_1101-436634	730	11	preprint	preprint	NN
10_1101-436634	730	12	(	(	-LRB-
10_1101-436634	730	13	which	which	WDT
10_1101-436634	730	14	was	be	VBD
10_1101-436634	730	15	notthis	notthis	DT
10_1101-436634	730	16	version	version	NN
10_1101-436634	730	17	posted	post	VBN
10_1101-436634	730	18	January	January	NNP
10_1101-436634	730	19	5	5	CD
10_1101-436634	730	20	,	,	,
10_1101-436634	730	21	2021	2021	CD
10_1101-436634	730	22	.	.	.
10_1101-436634	730	23	;	;	:
10_1101-436634	730	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	730	25	:	:	:
10_1101-436634	730	26	bioRxiv	biorxiv	VB
10_1101-436634	730	27	preprint	preprint	NN
10_1101-436634	730	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	730	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	730	30	38	38	CD
10_1101-436634	730	31	Supplementary	Supplementary	NNP
10_1101-436634	730	32	Figure	figure	NN
10_1101-436634	730	33	5	5	CD
10_1101-436634	730	34	:	:	:
10_1101-436634	730	35	Exonic	exonic	JJ
10_1101-436634	730	36	SNV	SNV	NNP
10_1101-436634	730	37	in	in	IN
10_1101-436634	730	38	LZTR1	lztr1	NN
10_1101-436634	730	39	associated	associate	VBN
10_1101-436634	730	40	with	with	IN
10_1101-436634	730	41	alternative	alternative	JJ
10_1101-436634	730	42	donor	donor	NN
10_1101-436634	730	43	usage	usage	NN
10_1101-436634	730	44	.	.	.
10_1101-436634	731	1	A	a	LS
10_1101-436634	731	2	)	)	-RRB-
10_1101-436634	731	3	IGV	igv	NN
10_1101-436634	731	4	snapshot	snapshot	NN
10_1101-436634	731	5	of	of	IN
10_1101-436634	731	6	a	a	DT
10_1101-436634	731	7	single	single	JJ
10_1101-436634	731	8	nucleotide	nucleotide	JJ
10_1101-436634	731	9	variant	variant	NN
10_1101-436634	731	10	(	(	-LRB-
10_1101-436634	731	11	GRCh38	GRCh38	NNP
10_1101-436634	731	12	,	,	,
10_1101-436634	731	13	chr22	chr22	NNS
10_1101-436634	731	14	:	:	:
10_1101-436634	731	15	g.20995026G	g.20995026G	NNP
10_1101-436634	731	16	>	>	XX
10_1101-436634	731	17	C	C	NNP
10_1101-436634	731	18	)	)	-RRB-
10_1101-436634	731	19	within	within	IN
10_1101-436634	731	20	an	an	DT
10_1101-436634	731	21	exon	exon	NN
10_1101-436634	731	22	of	of	IN
10_1101-436634	731	23	LZTR1	lztr1	NN
10_1101-436634	731	24	in	in	IN
10_1101-436634	731	25	LUAD	LUAD	NNP
10_1101-436634	731	26	sample	sample	NN
10_1101-436634	731	27	TCGA-38	tcga-38	JJ
10_1101-436634	731	28	-	-	HYPH
10_1101-436634	731	29	4631	4631	CD
10_1101-436634	731	30	-	-	HYPH
10_1101-436634	731	31	01A.	01A.	.
10_1101-436634	732	1	This	this	DT
10_1101-436634	732	2	variant	variant	NN
10_1101-436634	732	3	is	be	VBZ
10_1101-436634	732	4	associated	associate	VBN
10_1101-436634	732	5	with	with	IN
10_1101-436634	732	6	the	the	DT
10_1101-436634	732	7	formation	formation	NN
10_1101-436634	732	8	of	of	IN
10_1101-436634	732	9	an	an	DT
10_1101-436634	732	10	A	A	NNP
10_1101-436634	732	11	junction	junction	NN
10_1101-436634	732	12	,	,	,
10_1101-436634	732	13	JUNC00075013	JUNC00075013	NNP
10_1101-436634	732	14	,	,	,
10_1101-436634	732	15	which	which	WDT
10_1101-436634	732	16	has	have	VBZ
10_1101-436634	732	17	49	49	CD
10_1101-436634	732	18	reads	read	NNS
10_1101-436634	732	19	of	of	IN
10_1101-436634	732	20	support	support	NN
10_1101-436634	732	21	.	.	.
10_1101-436634	733	1	The	the	DT
10_1101-436634	733	2	variant	variant	NN
10_1101-436634	733	3	was	be	VBD
10_1101-436634	733	4	identified	identify	VBN
10_1101-436634	733	5	by	by	IN
10_1101-436634	733	6	RegTools	RegTools	NNP
10_1101-436634	733	7	,	,	,
10_1101-436634	733	8	VEP	VEP	NNP
10_1101-436634	733	9	,	,	,
10_1101-436634	733	10	and	and	CC
10_1101-436634	733	11	SpliceAI	SpliceAI	NNP
10_1101-436634	733	12	but	but	CC
10_1101-436634	733	13	no	no	DT
10_1101-436634	733	14	other	other	JJ
10_1101-436634	733	15	tools	tool	NNS
10_1101-436634	733	16	.	.	.
10_1101-436634	734	1	This	this	DT
10_1101-436634	734	2	result	result	NN
10_1101-436634	734	3	was	be	VBD
10_1101-436634	734	4	found	find	VBN
10_1101-436634	734	5	using	use	VBG
10_1101-436634	734	6	the	the	DT
10_1101-436634	734	7	default	default	NN
10_1101-436634	734	8	splice	splice	NN
10_1101-436634	734	9	variant	variant	JJ
10_1101-436634	734	10	window	window	NN
10_1101-436634	734	11	parameter	parameter	NN
10_1101-436634	734	12	(	(	-LRB-
10_1101-436634	734	13	i2e3	i2e3	ADD
10_1101-436634	734	14	)	)	-RRB-
10_1101-436634	734	15	.	.	.
10_1101-436634	735	1	B	b	NN
10_1101-436634	735	2	)	)	-RRB-
10_1101-436634	735	3	Sashimi	Sashimi	NNP
10_1101-436634	735	4	plot	plot	NN
10_1101-436634	735	5	visualization	visualization	NN
10_1101-436634	735	6	of	of	IN
10_1101-436634	735	7	the	the	DT
10_1101-436634	735	8	novel	novel	JJ
10_1101-436634	735	9	junction	junction	NN
10_1101-436634	735	10	.	.	.
10_1101-436634	736	1	.CC	.CC	NFP
10_1101-436634	736	2	-	-	:
10_1101-436634	736	3	BY	by	IN
10_1101-436634	736	4	-	-	HYPH
10_1101-436634	736	5	NC	NC	NNP
10_1101-436634	736	6	-	-	HYPH
10_1101-436634	736	7	ND	ND	NNP
10_1101-436634	736	8	4.0	4.0	CD
10_1101-436634	736	9	International	international	JJ
10_1101-436634	736	10	licensea	licensea	NNS
10_1101-436634	736	11	certified	certify	VBN
10_1101-436634	736	12	by	by	IN
10_1101-436634	736	13	peer	peer	NN
10_1101-436634	736	14	review	review	NN
10_1101-436634	736	15	)	)	-RRB-
10_1101-436634	736	16	is	be	VBZ
10_1101-436634	736	17	the	the	DT
10_1101-436634	736	18	author	author	NN
10_1101-436634	736	19	/	/	SYM
10_1101-436634	736	20	funder	funder	NN
10_1101-436634	736	21	,	,	,
10_1101-436634	736	22	who	who	WP
10_1101-436634	736	23	has	have	VBZ
10_1101-436634	736	24	granted	grant	VBN
10_1101-436634	736	25	bioRxiv	biorxiv	IN
10_1101-436634	736	26	a	a	DT
10_1101-436634	736	27	license	license	NN
10_1101-436634	736	28	to	to	TO
10_1101-436634	736	29	display	display	VB
10_1101-436634	736	30	the	the	DT
10_1101-436634	736	31	preprint	preprint	NN
10_1101-436634	736	32	in	in	IN
10_1101-436634	736	33	perpetuity	perpetuity	NN
10_1101-436634	736	34	.	.	.
10_1101-436634	737	1	It	-PRON-	PRP
10_1101-436634	737	2	is	be	VBZ
10_1101-436634	737	3	made	make	VBN
10_1101-436634	737	4	available	available	JJ
10_1101-436634	737	5	under	under	IN
10_1101-436634	737	6	The	the	DT
10_1101-436634	737	7	copyright	copyright	NN
10_1101-436634	737	8	holder	holder	NN
10_1101-436634	737	9	for	for	IN
10_1101-436634	737	10	this	this	DT
10_1101-436634	737	11	preprint	preprint	NN
10_1101-436634	737	12	(	(	-LRB-
10_1101-436634	737	13	which	which	WDT
10_1101-436634	737	14	was	be	VBD
10_1101-436634	737	15	notthis	notthis	DT
10_1101-436634	737	16	version	version	NN
10_1101-436634	737	17	posted	post	VBN
10_1101-436634	737	18	January	January	NNP
10_1101-436634	737	19	5	5	CD
10_1101-436634	737	20	,	,	,
10_1101-436634	737	21	2021	2021	CD
10_1101-436634	737	22	.	.	.
10_1101-436634	737	23	;	;	:
10_1101-436634	737	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	737	25	:	:	:
10_1101-436634	737	26	bioRxiv	biorxiv	VB
10_1101-436634	737	27	preprint	preprint	NN
10_1101-436634	737	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	737	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	737	30	39	39	CD
10_1101-436634	737	31	Supplementary	Supplementary	NNP
10_1101-436634	737	32	Figure	Figure	NNP
10_1101-436634	737	33	6	6	CD
10_1101-436634	737	34	.	.	.
10_1101-436634	738	1	Pan	pan	JJ
10_1101-436634	738	2	-	-	JJ
10_1101-436634	738	3	cancer	cancer	JJ
10_1101-436634	738	4	analysis	analysis	NN
10_1101-436634	738	5	of	of	IN
10_1101-436634	738	6	cohorts	cohort	NNS
10_1101-436634	738	7	from	from	IN
10_1101-436634	738	8	TCGA	TCGA	NNP
10_1101-436634	738	9	and	and	CC
10_1101-436634	738	10	MGI	MGI	NNP
10_1101-436634	738	11	reveals	reveal	VBZ
10_1101-436634	738	12	genes	gene	NNS
10_1101-436634	738	13	recurrently	recurrently	RB
10_1101-436634	738	14	disrupted	disrupt	VBN
10_1101-436634	738	15	by	by	IN
10_1101-436634	738	16	variants	variant	NNS
10_1101-436634	738	17	which	which	WDT
10_1101-436634	738	18	cause	cause	VBP
10_1101-436634	738	19	non	non	JJ
10_1101-436634	738	20	-	-	JJ
10_1101-436634	738	21	canonical	canonical	JJ
10_1101-436634	738	22	splicing	splicing	NN
10_1101-436634	738	23	patterns	pattern	NNS
10_1101-436634	738	24	Results	Results	NNPS
10_1101-436634	738	25	of	of	IN
10_1101-436634	738	26	analysis	analysis	NN
10_1101-436634	738	27	for	for	IN
10_1101-436634	738	28	recurrently	recurrently	RB
10_1101-436634	738	29	disrupted	disrupt	VBN
10_1101-436634	738	30	genes	gene	NNS
10_1101-436634	738	31	in	in	IN
10_1101-436634	738	32	each	each	DT
10_1101-436634	738	33	cohort	cohort	NN
10_1101-436634	738	34	.	.	.
10_1101-436634	739	1	A	a	LS
10_1101-436634	739	2	)	)	-RRB-
10_1101-436634	739	3	Rows	row	NNS
10_1101-436634	739	4	correspond	correspond	VBP
10_1101-436634	739	5	to	to	IN
10_1101-436634	739	6	the	the	DT
10_1101-436634	739	7	40	40	CD
10_1101-436634	739	8	most	most	RBS
10_1101-436634	739	9	frequently	frequently	RB
10_1101-436634	739	10	recurring	recur	VBG
10_1101-436634	739	11	genes	gene	NNS
10_1101-436634	739	12	,	,	,
10_1101-436634	739	13	as	as	IN
10_1101-436634	739	14	ranked	rank	VBN
10_1101-436634	739	15	by	by	IN
10_1101-436634	739	16	binomial	binomial	NNP
10_1101-436634	739	17	p	p	NN
10_1101-436634	739	18	-	-	HYPH
10_1101-436634	739	19	value	value	NN
10_1101-436634	739	20	.	.	.
10_1101-436634	740	1	Genes	gene	NNS
10_1101-436634	740	2	are	be	VBP
10_1101-436634	740	3	clustered	cluster	VBN
10_1101-436634	740	4	by	by	IN
10_1101-436634	740	5	whether	whether	IN
10_1101-436634	740	6	they	-PRON-	PRP
10_1101-436634	740	7	were	be	VBD
10_1101-436634	740	8	annotated	annotate	VBN
10_1101-436634	740	9	by	by	IN
10_1101-436634	740	10	the	the	DT
10_1101-436634	740	11	CGC	CGC	NNP
10_1101-436634	740	12	as	as	IN
10_1101-436634	740	13	an	an	DT
10_1101-436634	740	14	oncogene	oncogene	NN
10_1101-436634	740	15	(	(	-LRB-
10_1101-436634	740	16	red	red	NNP
10_1101-436634	740	17	)	)	-RRB-
10_1101-436634	740	18	,	,	,
10_1101-436634	740	19	an	an	DT
10_1101-436634	740	20	oncogene	oncogene	NN
10_1101-436634	740	21	and	and	CC
10_1101-436634	740	22	tumor	tumor	NN
10_1101-436634	740	23	suppressor	suppressor	NN
10_1101-436634	740	24	gene	gene	NN
10_1101-436634	740	25	(	(	-LRB-
10_1101-436634	740	26	yellow	yellow	NNP
10_1101-436634	740	27	)	)	-RRB-
10_1101-436634	740	28	,	,	,
10_1101-436634	740	29	a	a	DT
10_1101-436634	740	30	tumor	tumor	NN
10_1101-436634	740	31	suppressor	suppressor	NN
10_1101-436634	740	32	gene	gene	NN
10_1101-436634	740	33	(	(	-LRB-
10_1101-436634	740	34	green	green	NNP
10_1101-436634	740	35	)	)	-RRB-
10_1101-436634	740	36	,	,	,
10_1101-436634	740	37	or	or	CC
10_1101-436634	740	38	another	another	DT
10_1101-436634	740	39	type	type	NN
10_1101-436634	740	40	of	of	IN
10_1101-436634	740	41	cancer	cancer	NN
10_1101-436634	740	42	-	-	HYPH
10_1101-436634	740	43	relevant	relevant	JJ
10_1101-436634	740	44	gene	gene	NN
10_1101-436634	740	45	.	.	.
10_1101-436634	741	1	Shading	shade	VBG
10_1101-436634	741	2	corresponds	correspond	NNS
10_1101-436634	741	3	to	to	IN
10_1101-436634	741	4	−log10(p	−log10(p	ADD
10_1101-436634	741	5	value	value	NN
10_1101-436634	741	6	)	)	-RRB-
10_1101-436634	741	7	and	and	CC
10_1101-436634	741	8	columns	column	NNS
10_1101-436634	741	9	represent	represent	VBP
10_1101-436634	741	10	cancer	cancer	NN
10_1101-436634	741	11	types	type	NNS
10_1101-436634	741	12	.	.	.
10_1101-436634	742	1	Red	red	JJ
10_1101-436634	742	2	marks	mark	NNS
10_1101-436634	742	3	within	within	IN
10_1101-436634	742	4	cells	cell	NNS
10_1101-436634	742	5	indicate	indicate	VBP
10_1101-436634	742	6	that	that	IN
10_1101-436634	742	7	the	the	DT
10_1101-436634	742	8	gene	gene	NN
10_1101-436634	742	9	was	be	VBD
10_1101-436634	742	10	annotated	annotate	VBN
10_1101-436634	742	11	by	by	IN
10_1101-436634	742	12	CHASMplus	CHASMplus	NNP
10_1101-436634	742	13	as	as	IN
10_1101-436634	742	14	a	a	DT
10_1101-436634	742	15	driver	driver	NN
10_1101-436634	742	16	within	within	IN
10_1101-436634	742	17	a	a	DT
10_1101-436634	742	18	given	give	VBN
10_1101-436634	742	19	TCGA	tcga	NN
10_1101-436634	742	20	cohort	cohort	NN
10_1101-436634	742	21	.	.	.
10_1101-436634	743	1	B	b	NN
10_1101-436634	743	2	)	)	-RRB-
10_1101-436634	743	3	Rows	row	NNS
10_1101-436634	743	4	correspond	correspond	VB
10_1101-436634	743	5	to	to	IN
10_1101-436634	743	6	the	the	DT
10_1101-436634	743	7	40	40	CD
10_1101-436634	743	8	most	most	RBS
10_1101-436634	743	9	frequently	frequently	RB
10_1101-436634	743	10	recurring	recur	VBG
10_1101-436634	743	11	genes	gene	NNS
10_1101-436634	743	12	,	,	,
10_1101-436634	743	13	as	as	IN
10_1101-436634	743	14	ranked	rank	VBN
10_1101-436634	743	15	by	by	IN
10_1101-436634	743	16	fraction	fraction	NN
10_1101-436634	743	17	of	of	IN
10_1101-436634	743	18	samples	sample	NNS
10_1101-436634	743	19	.	.	.
10_1101-436634	744	1	Shading	shade	VBG
10_1101-436634	744	2	corresponds	correspond	NNS
10_1101-436634	744	3	to	to	IN
10_1101-436634	744	4	the	the	DT
10_1101-436634	744	5	fraction	fraction	NN
10_1101-436634	744	6	of	of	IN
10_1101-436634	744	7	samples	sample	NNS
10_1101-436634	744	8	and	and	CC
10_1101-436634	744	9	columns	column	NNS
10_1101-436634	744	10	represent	represent	VBP
10_1101-436634	744	11	cancer	cancer	NN
10_1101-436634	744	12	types	type	NNS
10_1101-436634	744	13	.	.	.
10_1101-436634	745	1	Red	red	JJ
10_1101-436634	745	2	marks	mark	NNS
10_1101-436634	745	3	within	within	IN
10_1101-436634	745	4	cells	cell	NNS
10_1101-436634	745	5	indicate	indicate	VBP
10_1101-436634	745	6	that	that	IN
10_1101-436634	745	7	the	the	DT
10_1101-436634	745	8	gene	gene	NN
10_1101-436634	745	9	was	be	VBD
10_1101-436634	745	10	annotated	annotate	VBN
10_1101-436634	745	11	by	by	IN
10_1101-436634	745	12	CHASMplus	CHASMplus	NNP
10_1101-436634	745	13	as	as	IN
10_1101-436634	745	14	a	a	DT
10_1101-436634	745	15	driver	driver	NN
10_1101-436634	745	16	within	within	IN
10_1101-436634	745	17	a	a	DT
10_1101-436634	745	18	given	give	VBN
10_1101-436634	745	19	TCGA	tcga	NN
10_1101-436634	745	20	cohort	cohort	NN
10_1101-436634	745	21	.	.	.
10_1101-436634	746	1	.CC	.CC	NFP
10_1101-436634	746	2	-	-	:
10_1101-436634	746	3	BY	by	IN
10_1101-436634	746	4	-	-	HYPH
10_1101-436634	746	5	NC	NC	NNP
10_1101-436634	746	6	-	-	HYPH
10_1101-436634	746	7	ND	ND	NNP
10_1101-436634	746	8	4.0	4.0	CD
10_1101-436634	746	9	International	international	JJ
10_1101-436634	746	10	licensea	licensea	NNS
10_1101-436634	746	11	certified	certify	VBN
10_1101-436634	746	12	by	by	IN
10_1101-436634	746	13	peer	peer	NN
10_1101-436634	746	14	review	review	NN
10_1101-436634	746	15	)	)	-RRB-
10_1101-436634	746	16	is	be	VBZ
10_1101-436634	746	17	the	the	DT
10_1101-436634	746	18	author	author	NN
10_1101-436634	746	19	/	/	SYM
10_1101-436634	746	20	funder	funder	NN
10_1101-436634	746	21	,	,	,
10_1101-436634	746	22	who	who	WP
10_1101-436634	746	23	has	have	VBZ
10_1101-436634	746	24	granted	grant	VBN
10_1101-436634	746	25	bioRxiv	biorxiv	IN
10_1101-436634	746	26	a	a	DT
10_1101-436634	746	27	license	license	NN
10_1101-436634	746	28	to	to	TO
10_1101-436634	746	29	display	display	VB
10_1101-436634	746	30	the	the	DT
10_1101-436634	746	31	preprint	preprint	NN
10_1101-436634	746	32	in	in	IN
10_1101-436634	746	33	perpetuity	perpetuity	NN
10_1101-436634	746	34	.	.	.
10_1101-436634	747	1	It	-PRON-	PRP
10_1101-436634	747	2	is	be	VBZ
10_1101-436634	747	3	made	make	VBN
10_1101-436634	747	4	available	available	JJ
10_1101-436634	747	5	under	under	IN
10_1101-436634	747	6	The	the	DT
10_1101-436634	747	7	copyright	copyright	NN
10_1101-436634	747	8	holder	holder	NN
10_1101-436634	747	9	for	for	IN
10_1101-436634	747	10	this	this	DT
10_1101-436634	747	11	preprint	preprint	NN
10_1101-436634	747	12	(	(	-LRB-
10_1101-436634	747	13	which	which	WDT
10_1101-436634	747	14	was	be	VBD
10_1101-436634	747	15	notthis	notthis	DT
10_1101-436634	747	16	version	version	NN
10_1101-436634	747	17	posted	post	VBN
10_1101-436634	747	18	January	January	NNP
10_1101-436634	747	19	5	5	CD
10_1101-436634	747	20	,	,	,
10_1101-436634	747	21	2021	2021	CD
10_1101-436634	747	22	.	.	.
10_1101-436634	747	23	;	;	:
10_1101-436634	747	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	747	25	:	:	:
10_1101-436634	747	26	bioRxiv	biorxiv	VB
10_1101-436634	747	27	preprint	preprint	NN
10_1101-436634	747	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	747	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	747	30	40	40	CD
10_1101-436634	747	31	Supplementary	Supplementary	NNP
10_1101-436634	747	32	Figure	Figure	NNP
10_1101-436634	747	33	7	7	CD
10_1101-436634	747	34	.	.	.
10_1101-436634	748	1	Pan	pan	JJ
10_1101-436634	748	2	-	-	JJ
10_1101-436634	748	3	cancer	cancer	JJ
10_1101-436634	748	4	analysis	analysis	NN
10_1101-436634	748	5	of	of	IN
10_1101-436634	748	6	cohorts	cohort	NNS
10_1101-436634	748	7	from	from	IN
10_1101-436634	748	8	TCGA	TCGA	NNP
10_1101-436634	748	9	and	and	CC
10_1101-436634	748	10	MGI	MGI	NNP
10_1101-436634	748	11	reveals	reveal	VBZ
10_1101-436634	748	12	genes	gene	NNS
10_1101-436634	748	13	recurrently	recurrently	RB
10_1101-436634	748	14	disrupted	disrupt	VBN
10_1101-436634	748	15	by	by	IN
10_1101-436634	748	16	variants	variant	NNS
10_1101-436634	748	17	which	which	WDT
10_1101-436634	748	18	promote	promote	VBP
10_1101-436634	748	19	splicing	splicing	NN
10_1101-436634	748	20	of	of	IN
10_1101-436634	748	21	particular	particular	JJ
10_1101-436634	748	22	canonical	canonical	JJ
10_1101-436634	748	23	junctions	junction	NNS
10_1101-436634	748	24	Results	Results	NNPS
10_1101-436634	748	25	of	of	IN
10_1101-436634	748	26	analysis	analysis	NN
10_1101-436634	748	27	for	for	IN
10_1101-436634	748	28	recurrently	recurrently	RB
10_1101-436634	748	29	disrupted	disrupt	VBN
10_1101-436634	748	30	genes	gene	NNS
10_1101-436634	748	31	in	in	IN
10_1101-436634	748	32	each	each	DT
10_1101-436634	748	33	cohort	cohort	NN
10_1101-436634	748	34	.	.	.
10_1101-436634	749	1	A	a	LS
10_1101-436634	749	2	)	)	-RRB-
10_1101-436634	749	3	Rows	row	NNS
10_1101-436634	749	4	correspond	correspond	VBP
10_1101-436634	749	5	to	to	IN
10_1101-436634	749	6	the	the	DT
10_1101-436634	749	7	40	40	CD
10_1101-436634	749	8	most	most	RBS
10_1101-436634	749	9	frequently	frequently	RB
10_1101-436634	749	10	recurring	recur	VBG
10_1101-436634	749	11	genes	gene	NNS
10_1101-436634	749	12	,	,	,
10_1101-436634	749	13	as	as	IN
10_1101-436634	749	14	ranked	rank	VBN
10_1101-436634	749	15	by	by	IN
10_1101-436634	749	16	binomial	binomial	NNP
10_1101-436634	749	17	p	p	NN
10_1101-436634	749	18	-	-	HYPH
10_1101-436634	749	19	value	value	NN
10_1101-436634	749	20	.	.	.
10_1101-436634	750	1	Genes	gene	NNS
10_1101-436634	750	2	are	be	VBP
10_1101-436634	750	3	clustered	cluster	VBN
10_1101-436634	750	4	by	by	IN
10_1101-436634	750	5	whether	whether	IN
10_1101-436634	750	6	they	-PRON-	PRP
10_1101-436634	750	7	were	be	VBD
10_1101-436634	750	8	annotated	annotate	VBN
10_1101-436634	750	9	by	by	IN
10_1101-436634	750	10	the	the	DT
10_1101-436634	750	11	CGC	CGC	NNP
10_1101-436634	750	12	as	as	IN
10_1101-436634	750	13	an	an	DT
10_1101-436634	750	14	oncogene	oncogene	NN
10_1101-436634	750	15	(	(	-LRB-
10_1101-436634	750	16	red	red	NNP
10_1101-436634	750	17	)	)	-RRB-
10_1101-436634	750	18	,	,	,
10_1101-436634	750	19	an	an	DT
10_1101-436634	750	20	oncogene	oncogene	NN
10_1101-436634	750	21	and	and	CC
10_1101-436634	750	22	tumor	tumor	NN
10_1101-436634	750	23	suppressor	suppressor	NN
10_1101-436634	750	24	gene	gene	NN
10_1101-436634	750	25	(	(	-LRB-
10_1101-436634	750	26	yellow	yellow	NNP
10_1101-436634	750	27	)	)	-RRB-
10_1101-436634	750	28	,	,	,
10_1101-436634	750	29	a	a	DT
10_1101-436634	750	30	tumor	tumor	NN
10_1101-436634	750	31	suppressor	suppressor	NN
10_1101-436634	750	32	gene	gene	NN
10_1101-436634	750	33	(	(	-LRB-
10_1101-436634	750	34	green	green	NNP
10_1101-436634	750	35	)	)	-RRB-
10_1101-436634	750	36	,	,	,
10_1101-436634	750	37	or	or	CC
10_1101-436634	750	38	another	another	DT
10_1101-436634	750	39	type	type	NN
10_1101-436634	750	40	of	of	IN
10_1101-436634	750	41	cancer	cancer	NN
10_1101-436634	750	42	-	-	HYPH
10_1101-436634	750	43	relevant	relevant	JJ
10_1101-436634	750	44	gene	gene	NN
10_1101-436634	750	45	.	.	.
10_1101-436634	751	1	Shading	shade	VBG
10_1101-436634	751	2	corresponds	correspond	NNS
10_1101-436634	751	3	to	to	IN
10_1101-436634	751	4	−log10(p	−log10(p	ADD
10_1101-436634	751	5	value	value	NN
10_1101-436634	751	6	)	)	-RRB-
10_1101-436634	751	7	and	and	CC
10_1101-436634	751	8	columns	column	NNS
10_1101-436634	751	9	represent	represent	VBP
10_1101-436634	751	10	cancer	cancer	NN
10_1101-436634	751	11	types	type	NNS
10_1101-436634	751	12	.	.	.
10_1101-436634	752	1	Red	red	JJ
10_1101-436634	752	2	marks	mark	NNS
10_1101-436634	752	3	within	within	IN
10_1101-436634	752	4	cells	cell	NNS
10_1101-436634	752	5	indicate	indicate	VBP
10_1101-436634	752	6	that	that	IN
10_1101-436634	752	7	the	the	DT
10_1101-436634	752	8	gene	gene	NN
10_1101-436634	752	9	was	be	VBD
10_1101-436634	752	10	annotated	annotate	VBN
10_1101-436634	752	11	by	by	IN
10_1101-436634	752	12	CHASMplus	CHASMplus	NNP
10_1101-436634	752	13	as	as	IN
10_1101-436634	752	14	a	a	DT
10_1101-436634	752	15	driver	driver	NN
10_1101-436634	752	16	within	within	IN
10_1101-436634	752	17	a	a	DT
10_1101-436634	752	18	given	give	VBN
10_1101-436634	752	19	TCGA	tcga	NN
10_1101-436634	752	20	cohort	cohort	NN
10_1101-436634	752	21	.	.	.
10_1101-436634	753	1	B	b	NN
10_1101-436634	753	2	)	)	-RRB-
10_1101-436634	753	3	Rows	row	NNS
10_1101-436634	753	4	correspond	correspond	VB
10_1101-436634	753	5	to	to	IN
10_1101-436634	753	6	the	the	DT
10_1101-436634	753	7	40	40	CD
10_1101-436634	753	8	most	most	RBS
10_1101-436634	753	9	frequently	frequently	RB
10_1101-436634	753	10	recurring	recur	VBG
10_1101-436634	753	11	genes	gene	NNS
10_1101-436634	753	12	,	,	,
10_1101-436634	753	13	as	as	IN
10_1101-436634	753	14	ranked	rank	VBN
10_1101-436634	753	15	by	by	IN
10_1101-436634	753	16	fraction	fraction	NN
10_1101-436634	753	17	of	of	IN
10_1101-436634	753	18	samples	sample	NNS
10_1101-436634	753	19	.	.	.
10_1101-436634	754	1	Shading	shade	VBG
10_1101-436634	754	2	corresponds	correspond	NNS
10_1101-436634	754	3	to	to	IN
10_1101-436634	754	4	the	the	DT
10_1101-436634	754	5	fraction	fraction	NN
10_1101-436634	754	6	of	of	IN
10_1101-436634	754	7	samples	sample	NNS
10_1101-436634	754	8	and	and	CC
10_1101-436634	754	9	columns	column	NNS
10_1101-436634	754	10	represent	represent	VBP
10_1101-436634	754	11	cancer	cancer	NN
10_1101-436634	754	12	types	type	NNS
10_1101-436634	754	13	.	.	.
10_1101-436634	755	1	Red	red	JJ
10_1101-436634	755	2	marks	mark	NNS
10_1101-436634	755	3	within	within	IN
10_1101-436634	755	4	cells	cell	NNS
10_1101-436634	755	5	indicate	indicate	VBP
10_1101-436634	755	6	that	that	IN
10_1101-436634	755	7	the	the	DT
10_1101-436634	755	8	gene	gene	NN
10_1101-436634	755	9	was	be	VBD
10_1101-436634	755	10	annotated	annotate	VBN
10_1101-436634	755	11	by	by	IN
10_1101-436634	755	12	CHASMplus	CHASMplus	NNP
10_1101-436634	755	13	as	as	IN
10_1101-436634	755	14	a	a	DT
10_1101-436634	755	15	driver	driver	NN
10_1101-436634	755	16	within	within	IN
10_1101-436634	755	17	a	a	DT
10_1101-436634	755	18	given	give	VBN
10_1101-436634	755	19	TCGA	tcga	NN
10_1101-436634	755	20	cohort	cohort	NN
10_1101-436634	755	21	.	.	.
10_1101-436634	756	1	.CC	.CC	NFP
10_1101-436634	756	2	-	-	:
10_1101-436634	756	3	BY	by	IN
10_1101-436634	756	4	-	-	HYPH
10_1101-436634	756	5	NC	NC	NNP
10_1101-436634	756	6	-	-	HYPH
10_1101-436634	756	7	ND	ND	NNP
10_1101-436634	756	8	4.0	4.0	CD
10_1101-436634	756	9	International	international	JJ
10_1101-436634	756	10	licensea	licensea	NNS
10_1101-436634	756	11	certified	certify	VBN
10_1101-436634	756	12	by	by	IN
10_1101-436634	756	13	peer	peer	NN
10_1101-436634	756	14	review	review	NN
10_1101-436634	756	15	)	)	-RRB-
10_1101-436634	756	16	is	be	VBZ
10_1101-436634	756	17	the	the	DT
10_1101-436634	756	18	author	author	NN
10_1101-436634	756	19	/	/	SYM
10_1101-436634	756	20	funder	funder	NN
10_1101-436634	756	21	,	,	,
10_1101-436634	756	22	who	who	WP
10_1101-436634	756	23	has	have	VBZ
10_1101-436634	756	24	granted	grant	VBN
10_1101-436634	756	25	bioRxiv	biorxiv	IN
10_1101-436634	756	26	a	a	DT
10_1101-436634	756	27	license	license	NN
10_1101-436634	756	28	to	to	TO
10_1101-436634	756	29	display	display	VB
10_1101-436634	756	30	the	the	DT
10_1101-436634	756	31	preprint	preprint	NN
10_1101-436634	756	32	in	in	IN
10_1101-436634	756	33	perpetuity	perpetuity	NN
10_1101-436634	756	34	.	.	.
10_1101-436634	757	1	It	-PRON-	PRP
10_1101-436634	757	2	is	be	VBZ
10_1101-436634	757	3	made	make	VBN
10_1101-436634	757	4	available	available	JJ
10_1101-436634	757	5	under	under	IN
10_1101-436634	757	6	The	the	DT
10_1101-436634	757	7	copyright	copyright	NN
10_1101-436634	757	8	holder	holder	NN
10_1101-436634	757	9	for	for	IN
10_1101-436634	757	10	this	this	DT
10_1101-436634	757	11	preprint	preprint	NN
10_1101-436634	757	12	(	(	-LRB-
10_1101-436634	757	13	which	which	WDT
10_1101-436634	757	14	was	be	VBD
10_1101-436634	757	15	notthis	notthis	DT
10_1101-436634	757	16	version	version	NN
10_1101-436634	757	17	posted	post	VBN
10_1101-436634	757	18	January	January	NNP
10_1101-436634	757	19	5	5	CD
10_1101-436634	757	20	,	,	,
10_1101-436634	757	21	2021	2021	CD
10_1101-436634	757	22	.	.	.
10_1101-436634	757	23	;	;	:
10_1101-436634	757	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	757	25	:	:	:
10_1101-436634	757	26	bioRxiv	biorxiv	VB
10_1101-436634	757	27	preprint	preprint	NN
10_1101-436634	757	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	757	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	757	30	41	41	CD
10_1101-436634	757	31	Supplementary	Supplementary	NNP
10_1101-436634	757	32	Figure	Figure	NNP
10_1101-436634	757	33	8	8	CD
10_1101-436634	757	34	.	.	.
10_1101-436634	758	1	TCGA	tcga	JJ
10_1101-436634	758	2	pan	pan	NN
10_1101-436634	758	3	-	-	HYPH
10_1101-436634	758	4	cancer	cancer	NN
10_1101-436634	758	5	analysis	analysis	NN
10_1101-436634	758	6	reveals	reveal	VBZ
10_1101-436634	758	7	genes	gene	NNS
10_1101-436634	758	8	recurrently	recurrently	RB
10_1101-436634	758	9	disrupted	disrupt	VBN
10_1101-436634	758	10	by	by	IN
10_1101-436634	758	11	variants	variant	NNS
10_1101-436634	758	12	which	which	WDT
10_1101-436634	758	13	cause	cause	VBP
10_1101-436634	758	14	non	non	JJ
10_1101-436634	758	15	-	-	JJ
10_1101-436634	758	16	canonical	canonical	JJ
10_1101-436634	758	17	splicing	splicing	NN
10_1101-436634	758	18	patterns	pattern	NNS
10_1101-436634	758	19	Results	Results	NNPS
10_1101-436634	758	20	of	of	IN
10_1101-436634	758	21	analysis	analysis	NN
10_1101-436634	758	22	for	for	IN
10_1101-436634	758	23	recurrently	recurrently	RB
10_1101-436634	758	24	disrupted	disrupt	VBN
10_1101-436634	758	25	genes	gene	NNS
10_1101-436634	758	26	in	in	IN
10_1101-436634	758	27	each	each	DT
10_1101-436634	758	28	TCGA	TCGA	NNP
10_1101-436634	758	29	cohort	cohort	NN
10_1101-436634	758	30	.	.	.
10_1101-436634	759	1	A	a	LS
10_1101-436634	759	2	)	)	-RRB-
10_1101-436634	759	3	Rows	row	NNS
10_1101-436634	759	4	correspond	correspond	VBP
10_1101-436634	759	5	to	to	IN
10_1101-436634	759	6	the	the	DT
10_1101-436634	759	7	40	40	CD
10_1101-436634	759	8	most	most	RBS
10_1101-436634	759	9	frequently	frequently	RB
10_1101-436634	759	10	recurring	recur	VBG
10_1101-436634	759	11	genes	gene	NNS
10_1101-436634	759	12	,	,	,
10_1101-436634	759	13	as	as	IN
10_1101-436634	759	14	ranked	rank	VBN
10_1101-436634	759	15	by	by	IN
10_1101-436634	759	16	binomial	binomial	NNP
10_1101-436634	759	17	p	p	NN
10_1101-436634	759	18	-	-	HYPH
10_1101-436634	759	19	value	value	NN
10_1101-436634	759	20	.	.	.
10_1101-436634	760	1	Genes	gene	NNS
10_1101-436634	760	2	are	be	VBP
10_1101-436634	760	3	clustered	cluster	VBN
10_1101-436634	760	4	by	by	IN
10_1101-436634	760	5	whether	whether	IN
10_1101-436634	760	6	they	-PRON-	PRP
10_1101-436634	760	7	were	be	VBD
10_1101-436634	760	8	annotated	annotate	VBN
10_1101-436634	760	9	by	by	IN
10_1101-436634	760	10	the	the	DT
10_1101-436634	760	11	CGC	CGC	NNP
10_1101-436634	760	12	as	as	IN
10_1101-436634	760	13	an	an	DT
10_1101-436634	760	14	oncogene	oncogene	NN
10_1101-436634	760	15	(	(	-LRB-
10_1101-436634	760	16	red	red	NNP
10_1101-436634	760	17	)	)	-RRB-
10_1101-436634	760	18	,	,	,
10_1101-436634	760	19	an	an	DT
10_1101-436634	760	20	oncogene	oncogene	NN
10_1101-436634	760	21	and	and	CC
10_1101-436634	760	22	tumor	tumor	NN
10_1101-436634	760	23	suppressor	suppressor	NN
10_1101-436634	760	24	gene	gene	NN
10_1101-436634	760	25	(	(	-LRB-
10_1101-436634	760	26	yellow	yellow	NNP
10_1101-436634	760	27	)	)	-RRB-
10_1101-436634	760	28	,	,	,
10_1101-436634	760	29	a	a	DT
10_1101-436634	760	30	tumor	tumor	NN
10_1101-436634	760	31	suppressor	suppressor	NN
10_1101-436634	760	32	gene	gene	NN
10_1101-436634	760	33	(	(	-LRB-
10_1101-436634	760	34	green	green	NNP
10_1101-436634	760	35	)	)	-RRB-
10_1101-436634	760	36	,	,	,
10_1101-436634	760	37	or	or	CC
10_1101-436634	760	38	another	another	DT
10_1101-436634	760	39	type	type	NN
10_1101-436634	760	40	of	of	IN
10_1101-436634	760	41	cancer	cancer	NN
10_1101-436634	760	42	-	-	HYPH
10_1101-436634	760	43	relevant	relevant	JJ
10_1101-436634	760	44	gene	gene	NN
10_1101-436634	760	45	.	.	.
10_1101-436634	761	1	Shading	shade	VBG
10_1101-436634	761	2	corresponds	correspond	NNS
10_1101-436634	761	3	to	to	IN
10_1101-436634	761	4	−log10(p	−log10(p	ADD
10_1101-436634	761	5	value	value	NN
10_1101-436634	761	6	)	)	-RRB-
10_1101-436634	761	7	and	and	CC
10_1101-436634	761	8	columns	column	NNS
10_1101-436634	761	9	represent	represent	VBP
10_1101-436634	761	10	cancer	cancer	NN
10_1101-436634	761	11	types	type	NNS
10_1101-436634	761	12	.	.	.
10_1101-436634	762	1	Red	red	JJ
10_1101-436634	762	2	marks	mark	NNS
10_1101-436634	762	3	within	within	IN
10_1101-436634	762	4	cells	cell	NNS
10_1101-436634	762	5	indicate	indicate	VBP
10_1101-436634	762	6	that	that	IN
10_1101-436634	762	7	the	the	DT
10_1101-436634	762	8	gene	gene	NN
10_1101-436634	762	9	was	be	VBD
10_1101-436634	762	10	annotated	annotate	VBN
10_1101-436634	762	11	by	by	IN
10_1101-436634	762	12	CHASMplus	CHASMplus	NNP
10_1101-436634	762	13	as	as	IN
10_1101-436634	762	14	a	a	DT
10_1101-436634	762	15	driver	driver	NN
10_1101-436634	762	16	within	within	IN
10_1101-436634	762	17	a	a	DT
10_1101-436634	762	18	given	give	VBN
10_1101-436634	762	19	TCGA	tcga	NN
10_1101-436634	762	20	cohort	cohort	NN
10_1101-436634	762	21	.	.	.
10_1101-436634	763	1	B	b	NN
10_1101-436634	763	2	)	)	-RRB-
10_1101-436634	763	3	Rows	row	NNS
10_1101-436634	763	4	correspond	correspond	VB
10_1101-436634	763	5	to	to	IN
10_1101-436634	763	6	the	the	DT
10_1101-436634	763	7	40	40	CD
10_1101-436634	763	8	most	most	RBS
10_1101-436634	763	9	frequently	frequently	RB
10_1101-436634	763	10	recurring	recur	VBG
10_1101-436634	763	11	genes	gene	NNS
10_1101-436634	763	12	,	,	,
10_1101-436634	763	13	as	as	IN
10_1101-436634	763	14	ranked	rank	VBN
10_1101-436634	763	15	by	by	IN
10_1101-436634	763	16	fraction	fraction	NN
10_1101-436634	763	17	of	of	IN
10_1101-436634	763	18	samples	sample	NNS
10_1101-436634	763	19	.	.	.
10_1101-436634	764	1	.CC	.CC	NFP
10_1101-436634	764	2	-	-	:
10_1101-436634	764	3	BY	by	IN
10_1101-436634	764	4	-	-	HYPH
10_1101-436634	764	5	NC	NC	NNP
10_1101-436634	764	6	-	-	HYPH
10_1101-436634	764	7	ND	ND	NNP
10_1101-436634	764	8	4.0	4.0	CD
10_1101-436634	764	9	International	international	JJ
10_1101-436634	764	10	licensea	licensea	NNS
10_1101-436634	764	11	certified	certify	VBN
10_1101-436634	764	12	by	by	IN
10_1101-436634	764	13	peer	peer	NN
10_1101-436634	764	14	review	review	NN
10_1101-436634	764	15	)	)	-RRB-
10_1101-436634	764	16	is	be	VBZ
10_1101-436634	764	17	the	the	DT
10_1101-436634	764	18	author	author	NN
10_1101-436634	764	19	/	/	SYM
10_1101-436634	764	20	funder	funder	NN
10_1101-436634	764	21	,	,	,
10_1101-436634	764	22	who	who	WP
10_1101-436634	764	23	has	have	VBZ
10_1101-436634	764	24	granted	grant	VBN
10_1101-436634	764	25	bioRxiv	biorxiv	IN
10_1101-436634	764	26	a	a	DT
10_1101-436634	764	27	license	license	NN
10_1101-436634	764	28	to	to	TO
10_1101-436634	764	29	display	display	VB
10_1101-436634	764	30	the	the	DT
10_1101-436634	764	31	preprint	preprint	NN
10_1101-436634	764	32	in	in	IN
10_1101-436634	764	33	perpetuity	perpetuity	NN
10_1101-436634	764	34	.	.	.
10_1101-436634	765	1	It	-PRON-	PRP
10_1101-436634	765	2	is	be	VBZ
10_1101-436634	765	3	made	make	VBN
10_1101-436634	765	4	available	available	JJ
10_1101-436634	765	5	under	under	IN
10_1101-436634	765	6	The	the	DT
10_1101-436634	765	7	copyright	copyright	NN
10_1101-436634	765	8	holder	holder	NN
10_1101-436634	765	9	for	for	IN
10_1101-436634	765	10	this	this	DT
10_1101-436634	765	11	preprint	preprint	NN
10_1101-436634	765	12	(	(	-LRB-
10_1101-436634	765	13	which	which	WDT
10_1101-436634	765	14	was	be	VBD
10_1101-436634	765	15	notthis	notthis	DT
10_1101-436634	765	16	version	version	NN
10_1101-436634	765	17	posted	post	VBN
10_1101-436634	765	18	January	January	NNP
10_1101-436634	765	19	5	5	CD
10_1101-436634	765	20	,	,	,
10_1101-436634	765	21	2021	2021	CD
10_1101-436634	765	22	.	.	.
10_1101-436634	765	23	;	;	:
10_1101-436634	765	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	765	25	:	:	:
10_1101-436634	765	26	bioRxiv	biorxiv	VB
10_1101-436634	765	27	preprint	preprint	NN
10_1101-436634	765	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	765	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	RB
10_1101-436634	765	30	42	42	CD
10_1101-436634	765	31	Shading	Shading	NNP
10_1101-436634	765	32	corresponds	correspond	NNS
10_1101-436634	765	33	to	to	IN
10_1101-436634	765	34	the	the	DT
10_1101-436634	765	35	fraction	fraction	NN
10_1101-436634	765	36	of	of	IN
10_1101-436634	765	37	samples	sample	NNS
10_1101-436634	765	38	and	and	CC
10_1101-436634	765	39	columns	column	NNS
10_1101-436634	765	40	represent	represent	VBP
10_1101-436634	765	41	cancer	cancer	NN
10_1101-436634	765	42	types	type	NNS
10_1101-436634	765	43	.	.	.
10_1101-436634	766	1	Red	red	JJ
10_1101-436634	766	2	marks	mark	NNS
10_1101-436634	766	3	within	within	IN
10_1101-436634	766	4	cells	cell	NNS
10_1101-436634	766	5	indicate	indicate	VBP
10_1101-436634	766	6	that	that	IN
10_1101-436634	766	7	the	the	DT
10_1101-436634	766	8	gene	gene	NN
10_1101-436634	766	9	was	be	VBD
10_1101-436634	766	10	annotated	annotate	VBN
10_1101-436634	766	11	by	by	IN
10_1101-436634	766	12	CHASMplus	CHASMplus	NNP
10_1101-436634	766	13	as	as	IN
10_1101-436634	766	14	a	a	DT
10_1101-436634	766	15	driver	driver	NN
10_1101-436634	766	16	within	within	IN
10_1101-436634	766	17	a	a	DT
10_1101-436634	766	18	given	give	VBN
10_1101-436634	766	19	TCGA	tcga	NN
10_1101-436634	766	20	cohort	cohort	NN
10_1101-436634	766	21	.	.	.
10_1101-436634	767	1	Supplementary	Supplementary	NNP
10_1101-436634	767	2	Figure	Figure	NNP
10_1101-436634	767	3	9	9	CD
10_1101-436634	767	4	.	.	.
10_1101-436634	768	1	TCGA	tcga	JJ
10_1101-436634	768	2	pan	pan	NN
10_1101-436634	768	3	-	-	HYPH
10_1101-436634	768	4	cancer	cancer	NN
10_1101-436634	768	5	analysis	analysis	NN
10_1101-436634	768	6	reveals	reveal	VBZ
10_1101-436634	768	7	genes	gene	NNS
10_1101-436634	768	8	recurrently	recurrently	RB
10_1101-436634	768	9	disrupted	disrupt	VBN
10_1101-436634	768	10	by	by	IN
10_1101-436634	768	11	variants	variant	NNS
10_1101-436634	768	12	which	which	WDT
10_1101-436634	768	13	promote	promote	VBP
10_1101-436634	768	14	splicing	splicing	NN
10_1101-436634	768	15	of	of	IN
10_1101-436634	768	16	particular	particular	JJ
10_1101-436634	768	17	canonical	canonical	JJ
10_1101-436634	768	18	junctions	junction	NNS
10_1101-436634	768	19	Results	Results	NNPS
10_1101-436634	768	20	of	of	IN
10_1101-436634	768	21	analysis	analysis	NN
10_1101-436634	768	22	for	for	IN
10_1101-436634	768	23	recurrently	recurrently	RB
10_1101-436634	768	24	disrupted	disrupt	VBN
10_1101-436634	768	25	genes	gene	NNS
10_1101-436634	768	26	in	in	IN
10_1101-436634	768	27	each	each	DT
10_1101-436634	768	28	TCGA	TCGA	NNP
10_1101-436634	768	29	cohort	cohort	NN
10_1101-436634	768	30	.	.	.
10_1101-436634	769	1	A	a	LS
10_1101-436634	769	2	)	)	-RRB-
10_1101-436634	769	3	Rows	row	NNS
10_1101-436634	769	4	correspond	correspond	VBP
10_1101-436634	769	5	to	to	IN
10_1101-436634	769	6	the	the	DT
10_1101-436634	769	7	40	40	CD
10_1101-436634	769	8	most	most	RBS
10_1101-436634	769	9	frequently	frequently	RB
10_1101-436634	769	10	recurring	recur	VBG
10_1101-436634	769	11	genes	gene	NNS
10_1101-436634	769	12	,	,	,
10_1101-436634	769	13	as	as	IN
10_1101-436634	769	14	ranked	rank	VBN
10_1101-436634	769	15	by	by	IN
10_1101-436634	769	16	binomial	binomial	NNP
10_1101-436634	769	17	p	p	NN
10_1101-436634	769	18	-	-	HYPH
10_1101-436634	769	19	value	value	NN
10_1101-436634	769	20	.	.	.
10_1101-436634	770	1	Genes	gene	NNS
10_1101-436634	770	2	are	be	VBP
10_1101-436634	770	3	clustered	cluster	VBN
10_1101-436634	770	4	by	by	IN
10_1101-436634	770	5	whether	whether	IN
10_1101-436634	770	6	they	-PRON-	PRP
10_1101-436634	770	7	were	be	VBD
10_1101-436634	770	8	annotated	annotate	VBN
10_1101-436634	770	9	by	by	IN
10_1101-436634	770	10	the	the	DT
10_1101-436634	770	11	CGC	CGC	NNP
10_1101-436634	770	12	as	as	IN
10_1101-436634	770	13	an	an	DT
10_1101-436634	770	14	oncogene	oncogene	NN
10_1101-436634	770	15	(	(	-LRB-
10_1101-436634	770	16	red	red	NNP
10_1101-436634	770	17	)	)	-RRB-
10_1101-436634	770	18	,	,	,
10_1101-436634	770	19	an	an	DT
10_1101-436634	770	20	oncogene	oncogene	NN
10_1101-436634	770	21	and	and	CC
10_1101-436634	770	22	tumor	tumor	NN
10_1101-436634	770	23	suppressor	suppressor	NN
10_1101-436634	770	24	gene	gene	NN
10_1101-436634	770	25	(	(	-LRB-
10_1101-436634	770	26	yellow	yellow	NNP
10_1101-436634	770	27	)	)	-RRB-
10_1101-436634	770	28	,	,	,
10_1101-436634	770	29	a	a	DT
10_1101-436634	770	30	tumor	tumor	NN
10_1101-436634	770	31	suppressor	suppressor	NN
10_1101-436634	770	32	gene	gene	NN
10_1101-436634	770	33	(	(	-LRB-
10_1101-436634	770	34	green	green	NNP
10_1101-436634	770	35	)	)	-RRB-
10_1101-436634	770	36	,	,	,
10_1101-436634	770	37	or	or	CC
10_1101-436634	770	38	another	another	DT
10_1101-436634	770	39	type	type	NN
10_1101-436634	770	40	of	of	IN
10_1101-436634	770	41	cancer	cancer	NN
10_1101-436634	770	42	-	-	HYPH
10_1101-436634	770	43	relevant	relevant	JJ
10_1101-436634	770	44	gene	gene	NN
10_1101-436634	770	45	.	.	.
10_1101-436634	771	1	Shading	shade	VBG
10_1101-436634	771	2	corresponds	correspond	NNS
10_1101-436634	771	3	to	to	IN
10_1101-436634	771	4	−log10(p	−log10(p	ADD
10_1101-436634	771	5	value	value	NN
10_1101-436634	771	6	)	)	-RRB-
10_1101-436634	771	7	and	and	CC
10_1101-436634	771	8	columns	column	NNS
10_1101-436634	771	9	represent	represent	VBP
10_1101-436634	771	10	cancer	cancer	NN
10_1101-436634	771	11	types	type	NNS
10_1101-436634	771	12	.	.	.
10_1101-436634	772	1	Red	red	JJ
10_1101-436634	772	2	marks	mark	NNS
10_1101-436634	772	3	within	within	IN
10_1101-436634	772	4	cells	cell	NNS
10_1101-436634	772	5	indicate	indicate	VBP
10_1101-436634	772	6	that	that	IN
10_1101-436634	772	7	the	the	DT
10_1101-436634	772	8	.CC	.CC	NFP
10_1101-436634	772	9	-	-	HYPH
10_1101-436634	772	10	BY	by	IN
10_1101-436634	772	11	-	-	HYPH
10_1101-436634	772	12	NC	NC	NNP
10_1101-436634	772	13	-	-	HYPH
10_1101-436634	772	14	ND	ND	NNP
10_1101-436634	772	15	4.0	4.0	CD
10_1101-436634	772	16	International	international	JJ
10_1101-436634	772	17	licensea	licensea	NNS
10_1101-436634	772	18	certified	certify	VBN
10_1101-436634	772	19	by	by	IN
10_1101-436634	772	20	peer	peer	NN
10_1101-436634	772	21	review	review	NN
10_1101-436634	772	22	)	)	-RRB-
10_1101-436634	772	23	is	be	VBZ
10_1101-436634	772	24	the	the	DT
10_1101-436634	772	25	author	author	NN
10_1101-436634	772	26	/	/	SYM
10_1101-436634	772	27	funder	funder	NN
10_1101-436634	772	28	,	,	,
10_1101-436634	772	29	who	who	WP
10_1101-436634	772	30	has	have	VBZ
10_1101-436634	772	31	granted	grant	VBN
10_1101-436634	772	32	bioRxiv	biorxiv	IN
10_1101-436634	772	33	a	a	DT
10_1101-436634	772	34	license	license	NN
10_1101-436634	772	35	to	to	TO
10_1101-436634	772	36	display	display	VB
10_1101-436634	772	37	the	the	DT
10_1101-436634	772	38	preprint	preprint	NN
10_1101-436634	772	39	in	in	IN
10_1101-436634	772	40	perpetuity	perpetuity	NN
10_1101-436634	772	41	.	.	.
10_1101-436634	773	1	It	-PRON-	PRP
10_1101-436634	773	2	is	be	VBZ
10_1101-436634	773	3	made	make	VBN
10_1101-436634	773	4	available	available	JJ
10_1101-436634	773	5	under	under	IN
10_1101-436634	773	6	The	the	DT
10_1101-436634	773	7	copyright	copyright	NN
10_1101-436634	773	8	holder	holder	NN
10_1101-436634	773	9	for	for	IN
10_1101-436634	773	10	this	this	DT
10_1101-436634	773	11	preprint	preprint	NN
10_1101-436634	773	12	(	(	-LRB-
10_1101-436634	773	13	which	which	WDT
10_1101-436634	773	14	was	be	VBD
10_1101-436634	773	15	notthis	notthis	DT
10_1101-436634	773	16	version	version	NN
10_1101-436634	773	17	posted	post	VBN
10_1101-436634	773	18	January	January	NNP
10_1101-436634	773	19	5	5	CD
10_1101-436634	773	20	,	,	,
10_1101-436634	773	21	2021	2021	CD
10_1101-436634	773	22	.	.	.
10_1101-436634	773	23	;	;	:
10_1101-436634	773	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	773	25	:	:	:
10_1101-436634	773	26	bioRxiv	biorxiv	VB
10_1101-436634	773	27	preprint	preprint	NN
10_1101-436634	773	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	773	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	773	30	43	43	CD
10_1101-436634	773	31	gene	gene	NN
10_1101-436634	773	32	was	be	VBD
10_1101-436634	773	33	annotated	annotate	VBN
10_1101-436634	773	34	by	by	IN
10_1101-436634	773	35	CHASMplus	CHASMplus	NNP
10_1101-436634	773	36	as	as	IN
10_1101-436634	773	37	a	a	DT
10_1101-436634	773	38	driver	driver	NN
10_1101-436634	773	39	within	within	IN
10_1101-436634	773	40	a	a	DT
10_1101-436634	773	41	given	give	VBN
10_1101-436634	773	42	TCGA	tcga	NN
10_1101-436634	773	43	cohort	cohort	NN
10_1101-436634	773	44	.	.	.
10_1101-436634	774	1	B	b	NN
10_1101-436634	774	2	)	)	-RRB-
10_1101-436634	774	3	Rows	row	NNS
10_1101-436634	774	4	correspond	correspond	VB
10_1101-436634	774	5	to	to	IN
10_1101-436634	774	6	the	the	DT
10_1101-436634	774	7	40	40	CD
10_1101-436634	774	8	most	most	RBS
10_1101-436634	774	9	frequently	frequently	RB
10_1101-436634	774	10	recurring	recur	VBG
10_1101-436634	774	11	genes	gene	NNS
10_1101-436634	774	12	,	,	,
10_1101-436634	774	13	as	as	IN
10_1101-436634	774	14	ranked	rank	VBN
10_1101-436634	774	15	by	by	IN
10_1101-436634	774	16	fraction	fraction	NN
10_1101-436634	774	17	of	of	IN
10_1101-436634	774	18	samples	sample	NNS
10_1101-436634	774	19	.	.	.
10_1101-436634	775	1	Shading	shade	VBG
10_1101-436634	775	2	corresponds	correspond	NNS
10_1101-436634	775	3	to	to	IN
10_1101-436634	775	4	the	the	DT
10_1101-436634	775	5	fraction	fraction	NN
10_1101-436634	775	6	of	of	IN
10_1101-436634	775	7	samples	sample	NNS
10_1101-436634	775	8	and	and	CC
10_1101-436634	775	9	columns	column	NNS
10_1101-436634	775	10	represent	represent	VBP
10_1101-436634	775	11	cancer	cancer	NN
10_1101-436634	775	12	types	type	NNS
10_1101-436634	775	13	.	.	.
10_1101-436634	776	1	Red	red	JJ
10_1101-436634	776	2	marks	mark	NNS
10_1101-436634	776	3	within	within	IN
10_1101-436634	776	4	cells	cell	NNS
10_1101-436634	776	5	indicate	indicate	VBP
10_1101-436634	776	6	that	that	IN
10_1101-436634	776	7	the	the	DT
10_1101-436634	776	8	gene	gene	NN
10_1101-436634	776	9	was	be	VBD
10_1101-436634	776	10	annotated	annotate	VBN
10_1101-436634	776	11	by	by	IN
10_1101-436634	776	12	CHASMplus	CHASMplus	NNP
10_1101-436634	776	13	as	as	IN
10_1101-436634	776	14	a	a	DT
10_1101-436634	776	15	driver	driver	NN
10_1101-436634	776	16	within	within	IN
10_1101-436634	776	17	a	a	DT
10_1101-436634	776	18	given	give	VBN
10_1101-436634	776	19	TCGA	tcga	NN
10_1101-436634	776	20	cohort	cohort	NN
10_1101-436634	776	21	.	.	.
10_1101-436634	777	1	Supplementary	Supplementary	NNP
10_1101-436634	777	2	Figure	Figure	NNP
10_1101-436634	777	3	10	10	CD
10_1101-436634	777	4	.	.	.
10_1101-436634	778	1	Analysis	Analysis	NNP
10_1101-436634	778	2	of	of	IN
10_1101-436634	778	3	HCC	HCC	NNP
10_1101-436634	778	4	,	,	,
10_1101-436634	778	5	OSCC	OSCC	NNP
10_1101-436634	778	6	,	,	,
10_1101-436634	778	7	and	and	CC
10_1101-436634	778	8	SCLC	SCLC	NNP
10_1101-436634	778	9	cohorts	cohort	NNS
10_1101-436634	778	10	reveals	reveal	VBZ
10_1101-436634	778	11	genes	gene	NNS
10_1101-436634	778	12	recurrently	recurrently	RB
10_1101-436634	778	13	disrupted	disrupt	VBN
10_1101-436634	778	14	by	by	IN
10_1101-436634	778	15	variants	variant	NNS
10_1101-436634	778	16	which	which	WDT
10_1101-436634	778	17	cause	cause	VBP
10_1101-436634	778	18	non	non	JJ
10_1101-436634	778	19	-	-	JJ
10_1101-436634	778	20	canonical	canonical	JJ
10_1101-436634	778	21	splicing	splicing	NN
10_1101-436634	778	22	patterns	pattern	NNS
10_1101-436634	778	23	Results	Results	NNPS
10_1101-436634	778	24	of	of	IN
10_1101-436634	778	25	analysis	analysis	NN
10_1101-436634	778	26	for	for	IN
10_1101-436634	778	27	recurrently	recurrently	RB
10_1101-436634	778	28	disrupted	disrupt	VBN
10_1101-436634	778	29	genes	gene	NNS
10_1101-436634	778	30	in	in	IN
10_1101-436634	778	31	each	each	DT
10_1101-436634	778	32	MGI	MGI	NNP
10_1101-436634	778	33	cohort	cohort	NN
10_1101-436634	778	34	.	.	.
10_1101-436634	779	1	A	a	LS
10_1101-436634	779	2	)	)	-RRB-
10_1101-436634	779	3	Rows	row	NNS
10_1101-436634	779	4	correspond	correspond	VB
10_1101-436634	779	5	to	to	IN
10_1101-436634	779	6	the	the	DT
10_1101-436634	779	7	3	3	CD
10_1101-436634	779	8	most	most	RBS
10_1101-436634	779	9	frequently	frequently	RB
10_1101-436634	779	10	recurring	recur	VBG
10_1101-436634	779	11	genes	gene	NNS
10_1101-436634	779	12	,	,	,
10_1101-436634	779	13	as	as	IN
10_1101-436634	779	14	ranked	rank	VBN
10_1101-436634	779	15	by	by	IN
10_1101-436634	779	16	binomial	binomial	NNP
10_1101-436634	779	17	p	p	NN
10_1101-436634	779	18	-	-	HYPH
10_1101-436634	779	19	value	value	NN
10_1101-436634	779	20	.	.	.
10_1101-436634	780	1	Shading	shade	VBG
10_1101-436634	780	2	corresponds	correspond	NNS
10_1101-436634	780	3	to	to	IN
10_1101-436634	780	4	−log10(p	−log10(p	ADD
10_1101-436634	780	5	value	value	NN
10_1101-436634	780	6	)	)	-RRB-
10_1101-436634	780	7	and	and	CC
10_1101-436634	780	8	columns	column	NNS
10_1101-436634	780	9	represent	represent	VBP
10_1101-436634	780	10	cancer	cancer	NN
10_1101-436634	780	11	types	type	NNS
10_1101-436634	780	12	.	.	.
10_1101-436634	781	1	B	b	NN
10_1101-436634	781	2	)	)	-RRB-
10_1101-436634	781	3	Rows	row	NNS
10_1101-436634	781	4	correspond	correspond	VB
10_1101-436634	781	5	to	to	IN
10_1101-436634	781	6	the	the	DT
10_1101-436634	781	7	3	3	CD
10_1101-436634	781	8	most	most	RBS
10_1101-436634	781	9	frequently	frequently	RB
10_1101-436634	781	10	recurring	recur	VBG
10_1101-436634	781	11	genes	gene	NNS
10_1101-436634	781	12	,	,	,
10_1101-436634	781	13	as	as	IN
10_1101-436634	781	14	ranked	rank	VBN
10_1101-436634	781	15	by	by	IN
10_1101-436634	781	16	fraction	fraction	NN
10_1101-436634	781	17	of	of	IN
10_1101-436634	781	18	samples	sample	NNS
10_1101-436634	781	19	.	.	.
10_1101-436634	782	1	Shading	shade	VBG
10_1101-436634	782	2	corresponds	correspond	NNS
10_1101-436634	782	3	to	to	IN
10_1101-436634	782	4	the	the	DT
10_1101-436634	782	5	fraction	fraction	NN
10_1101-436634	782	6	of	of	IN
10_1101-436634	782	7	samples	sample	NNS
10_1101-436634	782	8	and	and	CC
10_1101-436634	782	9	columns	column	NNS
10_1101-436634	782	10	represent	represent	VBP
10_1101-436634	782	11	cancer	cancer	NN
10_1101-436634	782	12	types	type	NNS
10_1101-436634	782	13	.	.	.
10_1101-436634	783	1	.CC	.CC	NFP
10_1101-436634	783	2	-	-	:
10_1101-436634	783	3	BY	by	IN
10_1101-436634	783	4	-	-	HYPH
10_1101-436634	783	5	NC	NC	NNP
10_1101-436634	783	6	-	-	HYPH
10_1101-436634	783	7	ND	ND	NNP
10_1101-436634	783	8	4.0	4.0	CD
10_1101-436634	783	9	International	international	JJ
10_1101-436634	783	10	licensea	licensea	NNS
10_1101-436634	783	11	certified	certify	VBN
10_1101-436634	783	12	by	by	IN
10_1101-436634	783	13	peer	peer	NN
10_1101-436634	783	14	review	review	NN
10_1101-436634	783	15	)	)	-RRB-
10_1101-436634	783	16	is	be	VBZ
10_1101-436634	783	17	the	the	DT
10_1101-436634	783	18	author	author	NN
10_1101-436634	783	19	/	/	SYM
10_1101-436634	783	20	funder	funder	NN
10_1101-436634	783	21	,	,	,
10_1101-436634	783	22	who	who	WP
10_1101-436634	783	23	has	have	VBZ
10_1101-436634	783	24	granted	grant	VBN
10_1101-436634	783	25	bioRxiv	biorxiv	IN
10_1101-436634	783	26	a	a	DT
10_1101-436634	783	27	license	license	NN
10_1101-436634	783	28	to	to	TO
10_1101-436634	783	29	display	display	VB
10_1101-436634	783	30	the	the	DT
10_1101-436634	783	31	preprint	preprint	NN
10_1101-436634	783	32	in	in	IN
10_1101-436634	783	33	perpetuity	perpetuity	NN
10_1101-436634	783	34	.	.	.
10_1101-436634	784	1	It	-PRON-	PRP
10_1101-436634	784	2	is	be	VBZ
10_1101-436634	784	3	made	make	VBN
10_1101-436634	784	4	available	available	JJ
10_1101-436634	784	5	under	under	IN
10_1101-436634	784	6	The	the	DT
10_1101-436634	784	7	copyright	copyright	NN
10_1101-436634	784	8	holder	holder	NN
10_1101-436634	784	9	for	for	IN
10_1101-436634	784	10	this	this	DT
10_1101-436634	784	11	preprint	preprint	NN
10_1101-436634	784	12	(	(	-LRB-
10_1101-436634	784	13	which	which	WDT
10_1101-436634	784	14	was	be	VBD
10_1101-436634	784	15	notthis	notthis	DT
10_1101-436634	784	16	version	version	NN
10_1101-436634	784	17	posted	post	VBN
10_1101-436634	784	18	January	January	NNP
10_1101-436634	784	19	5	5	CD
10_1101-436634	784	20	,	,	,
10_1101-436634	784	21	2021	2021	CD
10_1101-436634	784	22	.	.	.
10_1101-436634	784	23	;	;	:
10_1101-436634	784	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	784	25	:	:	:
10_1101-436634	784	26	bioRxiv	biorxiv	VB
10_1101-436634	784	27	preprint	preprint	NN
10_1101-436634	784	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	784	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	784	30	44	44	CD
10_1101-436634	784	31	Supplementary	Supplementary	NNP
10_1101-436634	784	32	Figure	Figure	NNP
10_1101-436634	784	33	11	11	CD
10_1101-436634	784	34	.	.	.
10_1101-436634	785	1	Analysis	Analysis	NNP
10_1101-436634	785	2	of	of	IN
10_1101-436634	785	3	HCC	HCC	NNP
10_1101-436634	785	4	,	,	,
10_1101-436634	785	5	OSCC	OSCC	NNP
10_1101-436634	785	6	,	,	,
10_1101-436634	785	7	and	and	CC
10_1101-436634	785	8	SCLC	SCLC	NNP
10_1101-436634	785	9	cohorts	cohort	NNS
10_1101-436634	785	10	reveals	reveal	VBZ
10_1101-436634	785	11	genes	gene	NNS
10_1101-436634	785	12	recurrently	recurrently	RB
10_1101-436634	785	13	disrupted	disrupt	VBN
10_1101-436634	785	14	by	by	IN
10_1101-436634	785	15	variants	variant	NNS
10_1101-436634	785	16	which	which	WDT
10_1101-436634	785	17	promote	promote	VBP
10_1101-436634	785	18	splicing	splicing	NN
10_1101-436634	785	19	of	of	IN
10_1101-436634	785	20	particular	particular	JJ
10_1101-436634	785	21	canonical	canonical	JJ
10_1101-436634	785	22	junctions	junction	NNS
10_1101-436634	785	23	Results	Results	NNPS
10_1101-436634	785	24	of	of	IN
10_1101-436634	785	25	analysis	analysis	NN
10_1101-436634	785	26	for	for	IN
10_1101-436634	785	27	recurrently	recurrently	RB
10_1101-436634	785	28	disrupted	disrupt	VBN
10_1101-436634	785	29	genes	gene	NNS
10_1101-436634	785	30	in	in	IN
10_1101-436634	785	31	each	each	DT
10_1101-436634	785	32	TCGA	TCGA	NNP
10_1101-436634	785	33	cohort	cohort	NN
10_1101-436634	785	34	.	.	.
10_1101-436634	786	1	A	a	LS
10_1101-436634	786	2	)	)	-RRB-
10_1101-436634	786	3	Rows	row	NNS
10_1101-436634	786	4	correspond	correspond	VB
10_1101-436634	786	5	to	to	IN
10_1101-436634	786	6	the	the	DT
10_1101-436634	786	7	4	4	CD
10_1101-436634	786	8	most	most	RBS
10_1101-436634	786	9	frequently	frequently	RB
10_1101-436634	786	10	recurring	recur	VBG
10_1101-436634	786	11	genes	gene	NNS
10_1101-436634	786	12	,	,	,
10_1101-436634	786	13	as	as	IN
10_1101-436634	786	14	ranked	rank	VBN
10_1101-436634	786	15	by	by	IN
10_1101-436634	786	16	binomial	binomial	NNP
10_1101-436634	786	17	p	p	NN
10_1101-436634	786	18	-	-	HYPH
10_1101-436634	786	19	value	value	NN
10_1101-436634	786	20	.	.	.
10_1101-436634	787	1	Shading	shade	VBG
10_1101-436634	787	2	corresponds	correspond	NNS
10_1101-436634	787	3	to	to	IN
10_1101-436634	787	4	−log10(p	−log10(p	ADD
10_1101-436634	787	5	value	value	NN
10_1101-436634	787	6	)	)	-RRB-
10_1101-436634	787	7	and	and	CC
10_1101-436634	787	8	columns	column	NNS
10_1101-436634	787	9	represent	represent	VBP
10_1101-436634	787	10	cancer	cancer	NN
10_1101-436634	787	11	types	type	NNS
10_1101-436634	787	12	.	.	.
10_1101-436634	788	1	B	b	NN
10_1101-436634	788	2	)	)	-RRB-
10_1101-436634	788	3	Rows	row	NNS
10_1101-436634	788	4	correspond	correspond	VB
10_1101-436634	788	5	to	to	IN
10_1101-436634	788	6	the	the	DT
10_1101-436634	788	7	4	4	CD
10_1101-436634	788	8	most	most	RBS
10_1101-436634	788	9	frequently	frequently	RB
10_1101-436634	788	10	recurring	recur	VBG
10_1101-436634	788	11	genes	gene	NNS
10_1101-436634	788	12	,	,	,
10_1101-436634	788	13	as	as	IN
10_1101-436634	788	14	ranked	rank	VBN
10_1101-436634	788	15	by	by	IN
10_1101-436634	788	16	fraction	fraction	NN
10_1101-436634	788	17	of	of	IN
10_1101-436634	788	18	samples	sample	NNS
10_1101-436634	788	19	.	.	.
10_1101-436634	789	1	Shading	shade	VBG
10_1101-436634	789	2	corresponds	correspond	NNS
10_1101-436634	789	3	to	to	IN
10_1101-436634	789	4	the	the	DT
10_1101-436634	789	5	fraction	fraction	NN
10_1101-436634	789	6	of	of	IN
10_1101-436634	789	7	samples	sample	NNS
10_1101-436634	789	8	and	and	CC
10_1101-436634	789	9	columns	column	NNS
10_1101-436634	789	10	represent	represent	VBP
10_1101-436634	789	11	cancer	cancer	NN
10_1101-436634	789	12	types	type	NNS
10_1101-436634	789	13	.	.	.
10_1101-436634	790	1	.CC	.CC	NFP
10_1101-436634	790	2	-	-	:
10_1101-436634	790	3	BY	by	IN
10_1101-436634	790	4	-	-	HYPH
10_1101-436634	790	5	NC	NC	NNP
10_1101-436634	790	6	-	-	HYPH
10_1101-436634	790	7	ND	ND	NNP
10_1101-436634	790	8	4.0	4.0	CD
10_1101-436634	790	9	International	international	JJ
10_1101-436634	790	10	licensea	licensea	NNS
10_1101-436634	790	11	certified	certify	VBN
10_1101-436634	790	12	by	by	IN
10_1101-436634	790	13	peer	peer	NN
10_1101-436634	790	14	review	review	NN
10_1101-436634	790	15	)	)	-RRB-
10_1101-436634	790	16	is	be	VBZ
10_1101-436634	790	17	the	the	DT
10_1101-436634	790	18	author	author	NN
10_1101-436634	790	19	/	/	SYM
10_1101-436634	790	20	funder	funder	NN
10_1101-436634	790	21	,	,	,
10_1101-436634	790	22	who	who	WP
10_1101-436634	790	23	has	have	VBZ
10_1101-436634	790	24	granted	grant	VBN
10_1101-436634	790	25	bioRxiv	biorxiv	IN
10_1101-436634	790	26	a	a	DT
10_1101-436634	790	27	license	license	NN
10_1101-436634	790	28	to	to	TO
10_1101-436634	790	29	display	display	VB
10_1101-436634	790	30	the	the	DT
10_1101-436634	790	31	preprint	preprint	NN
10_1101-436634	790	32	in	in	IN
10_1101-436634	790	33	perpetuity	perpetuity	NN
10_1101-436634	790	34	.	.	.
10_1101-436634	791	1	It	-PRON-	PRP
10_1101-436634	791	2	is	be	VBZ
10_1101-436634	791	3	made	make	VBN
10_1101-436634	791	4	available	available	JJ
10_1101-436634	791	5	under	under	IN
10_1101-436634	791	6	The	the	DT
10_1101-436634	791	7	copyright	copyright	NN
10_1101-436634	791	8	holder	holder	NN
10_1101-436634	791	9	for	for	IN
10_1101-436634	791	10	this	this	DT
10_1101-436634	791	11	preprint	preprint	NN
10_1101-436634	791	12	(	(	-LRB-
10_1101-436634	791	13	which	which	WDT
10_1101-436634	791	14	was	be	VBD
10_1101-436634	791	15	notthis	notthis	DT
10_1101-436634	791	16	version	version	NN
10_1101-436634	791	17	posted	post	VBN
10_1101-436634	791	18	January	January	NNP
10_1101-436634	791	19	5	5	CD
10_1101-436634	791	20	,	,	,
10_1101-436634	791	21	2021	2021	CD
10_1101-436634	791	22	.	.	.
10_1101-436634	791	23	;	;	:
10_1101-436634	791	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	791	25	:	:	:
10_1101-436634	791	26	bioRxiv	biorxiv	VB
10_1101-436634	791	27	preprint	preprint	NN
10_1101-436634	791	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	791	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	791	30	45	45	CD
10_1101-436634	791	31	Supplementary	Supplementary	NNP
10_1101-436634	791	32	Figure	Figure	NNP
10_1101-436634	791	33	12	12	CD
10_1101-436634	791	34	:	:	:
10_1101-436634	791	35	Intronic	intronic	JJ
10_1101-436634	791	36	SNV	SNV	NNP
10_1101-436634	791	37	in	in	IN
10_1101-436634	791	38	TP53	TP53	NNP
10_1101-436634	791	39	associated	associate	VBN
10_1101-436634	791	40	with	with	IN
10_1101-436634	791	41	alternative	alternative	JJ
10_1101-436634	791	42	donor	donor	NN
10_1101-436634	791	43	usage	usage	NN
10_1101-436634	791	44	.	.	.
10_1101-436634	792	1	A	a	LS
10_1101-436634	792	2	)	)	-RRB-
10_1101-436634	792	3	IGV	igv	NN
10_1101-436634	792	4	snapshot	snapshot	NN
10_1101-436634	792	5	of	of	IN
10_1101-436634	792	6	a	a	DT
10_1101-436634	792	7	single	single	JJ
10_1101-436634	792	8	nucleotide	nucleotide	JJ
10_1101-436634	792	9	variant	variant	NN
10_1101-436634	792	10	(	(	-LRB-
10_1101-436634	792	11	GRCh38	grch38	NN
10_1101-436634	792	12	,	,	,
10_1101-436634	792	13	chr17	chr17	NN
10_1101-436634	792	14	:	:	:
10_1101-436634	792	15	g.7673609C	g.7673609c	XX
10_1101-436634	792	16	>	>	XX
10_1101-436634	792	17	A	a	NN
10_1101-436634	792	18	)	)	-RRB-
10_1101-436634	792	19	within	within	IN
10_1101-436634	792	20	an	an	DT
10_1101-436634	792	21	intron	intron	NN
10_1101-436634	792	22	of	of	IN
10_1101-436634	792	23	TP53	TP53	NNP
10_1101-436634	792	24	in	in	IN
10_1101-436634	792	25	an	an	DT
10_1101-436634	792	26	OSCC	OSCC	NNP
10_1101-436634	792	27	sample	sample	NN
10_1101-436634	792	28	.	.	.
10_1101-436634	793	1	This	this	DT
10_1101-436634	793	2	variant	variant	NN
10_1101-436634	793	3	is	be	VBZ
10_1101-436634	793	4	associated	associate	VBN
10_1101-436634	793	5	with	with	IN
10_1101-436634	793	6	an	an	DT
10_1101-436634	793	7	exon	exon	JJ
10_1101-436634	793	8	skipping	skipping	NN
10_1101-436634	793	9	event	event	NN
10_1101-436634	793	10	with	with	IN
10_1101-436634	793	11	23	23	CD
10_1101-436634	793	12	reads	read	NNS
10_1101-436634	793	13	of	of	IN
10_1101-436634	793	14	support	support	NN
10_1101-436634	793	15	and	and	CC
10_1101-436634	793	16	an	an	DT
10_1101-436634	793	17	alternate	alternate	JJ
10_1101-436634	793	18	acceptor	acceptor	NN
10_1101-436634	793	19	site	site	NN
10_1101-436634	793	20	usage	usage	NN
10_1101-436634	793	21	with	with	IN
10_1101-436634	793	22	41	41	CD
10_1101-436634	793	23	reads	read	NNS
10_1101-436634	793	24	of	of	IN
10_1101-436634	793	25	support	support	NN
10_1101-436634	793	26	.	.	.
10_1101-436634	794	1	This	this	DT
10_1101-436634	794	2	result	result	NN
10_1101-436634	794	3	was	be	VBD
10_1101-436634	794	4	found	find	VBN
10_1101-436634	794	5	using	use	VBG
10_1101-436634	794	6	the	the	DT
10_1101-436634	794	7	default	default	NN
10_1101-436634	794	8	splice	splice	NN
10_1101-436634	794	9	variant	variant	JJ
10_1101-436634	794	10	window	window	NN
10_1101-436634	794	11	parameter	parameter	NN
10_1101-436634	794	12	(	(	-LRB-
10_1101-436634	794	13	i2e3	i2e3	ADD
10_1101-436634	794	14	)	)	-RRB-
10_1101-436634	794	15	.	.	.
10_1101-436634	795	1	B	b	NN
10_1101-436634	795	2	)	)	-RRB-
10_1101-436634	795	3	Sashimi	Sashimi	NNP
10_1101-436634	795	4	plot	plot	NN
10_1101-436634	795	5	visualization	visualization	NN
10_1101-436634	795	6	of	of	IN
10_1101-436634	795	7	the	the	DT
10_1101-436634	795	8	novel	novel	JJ
10_1101-436634	795	9	junction	junction	NN
10_1101-436634	795	10	.	.	.
10_1101-436634	796	1	.CC	.CC	NFP
10_1101-436634	796	2	-	-	:
10_1101-436634	796	3	BY	by	IN
10_1101-436634	796	4	-	-	HYPH
10_1101-436634	796	5	NC	NC	NNP
10_1101-436634	796	6	-	-	HYPH
10_1101-436634	796	7	ND	ND	NNP
10_1101-436634	796	8	4.0	4.0	CD
10_1101-436634	796	9	International	international	JJ
10_1101-436634	796	10	licensea	licensea	NNS
10_1101-436634	796	11	certified	certify	VBN
10_1101-436634	796	12	by	by	IN
10_1101-436634	796	13	peer	peer	NN
10_1101-436634	796	14	review	review	NN
10_1101-436634	796	15	)	)	-RRB-
10_1101-436634	796	16	is	be	VBZ
10_1101-436634	796	17	the	the	DT
10_1101-436634	796	18	author	author	NN
10_1101-436634	796	19	/	/	SYM
10_1101-436634	796	20	funder	funder	NN
10_1101-436634	796	21	,	,	,
10_1101-436634	796	22	who	who	WP
10_1101-436634	796	23	has	have	VBZ
10_1101-436634	796	24	granted	grant	VBN
10_1101-436634	796	25	bioRxiv	biorxiv	IN
10_1101-436634	796	26	a	a	DT
10_1101-436634	796	27	license	license	NN
10_1101-436634	796	28	to	to	TO
10_1101-436634	796	29	display	display	VB
10_1101-436634	796	30	the	the	DT
10_1101-436634	796	31	preprint	preprint	NN
10_1101-436634	796	32	in	in	IN
10_1101-436634	796	33	perpetuity	perpetuity	NN
10_1101-436634	796	34	.	.	.
10_1101-436634	797	1	It	-PRON-	PRP
10_1101-436634	797	2	is	be	VBZ
10_1101-436634	797	3	made	make	VBN
10_1101-436634	797	4	available	available	JJ
10_1101-436634	797	5	under	under	IN
10_1101-436634	797	6	The	the	DT
10_1101-436634	797	7	copyright	copyright	NN
10_1101-436634	797	8	holder	holder	NN
10_1101-436634	797	9	for	for	IN
10_1101-436634	797	10	this	this	DT
10_1101-436634	797	11	preprint	preprint	NN
10_1101-436634	797	12	(	(	-LRB-
10_1101-436634	797	13	which	which	WDT
10_1101-436634	797	14	was	be	VBD
10_1101-436634	797	15	notthis	notthis	DT
10_1101-436634	797	16	version	version	NN
10_1101-436634	797	17	posted	post	VBN
10_1101-436634	797	18	January	January	NNP
10_1101-436634	797	19	5	5	CD
10_1101-436634	797	20	,	,	,
10_1101-436634	797	21	2021	2021	CD
10_1101-436634	797	22	.	.	.
10_1101-436634	797	23	;	;	:
10_1101-436634	797	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	797	25	:	:	:
10_1101-436634	797	26	bioRxiv	biorxiv	VB
10_1101-436634	797	27	preprint	preprint	NN
10_1101-436634	797	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	797	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NN
10_1101-436634	797	30	46	46	CD
10_1101-436634	797	31	Supplementary	Supplementary	NNP
10_1101-436634	797	32	Figure	Figure	NNP
10_1101-436634	797	33	13	13	CD
10_1101-436634	797	34	:	:	:
10_1101-436634	797	35	Intronic	intronic	JJ
10_1101-436634	797	36	deletion	deletion	NN
10_1101-436634	797	37	in	in	IN
10_1101-436634	797	38	RNF145	RNF145	NNP
10_1101-436634	797	39	associated	associate	VBN
10_1101-436634	797	40	with	with	IN
10_1101-436634	797	41	alternative	alternative	JJ
10_1101-436634	797	42	donor	donor	NN
10_1101-436634	797	43	usage	usage	NN
10_1101-436634	797	44	.	.	.
10_1101-436634	798	1	A	a	LS
10_1101-436634	798	2	)	)	-RRB-
10_1101-436634	798	3	IGV	igv	NN
10_1101-436634	798	4	snapshot	snapshot	NN
10_1101-436634	798	5	of	of	IN
10_1101-436634	798	6	a	a	DT
10_1101-436634	798	7	single	single	JJ
10_1101-436634	798	8	nucleotide	nucleotide	JJ
10_1101-436634	798	9	variant	variant	NN
10_1101-436634	798	10	(	(	-LRB-
10_1101-436634	798	11	GRCh38	GRCh38	NNP
10_1101-436634	798	12	,	,	,
10_1101-436634	798	13	chr5	chr5	NN
10_1101-436634	798	14	:	:	:
10_1101-436634	798	15	g.159169058delA	g.159169058delA	NNP
10_1101-436634	798	16	)	)	-RRB-
10_1101-436634	798	17	within	within	IN
10_1101-436634	798	18	an	an	DT
10_1101-436634	798	19	intron	intron	NN
10_1101-436634	798	20	of	of	IN
10_1101-436634	798	21	RNF145	RNF145	NNP
10_1101-436634	798	22	in	in	IN
10_1101-436634	798	23	COAD	COAD	NNP
10_1101-436634	798	24	samples	sample	NNS
10_1101-436634	798	25	.	.	.
10_1101-436634	799	1	This	this	DT
10_1101-436634	799	2	variant	variant	NN
10_1101-436634	799	3	is	be	VBZ
10_1101-436634	799	4	associated	associate	VBN
10_1101-436634	799	5	with	with	IN
10_1101-436634	799	6	an	an	DT
10_1101-436634	799	7	exon	exon	JJ
10_1101-436634	799	8	skipping	skipping	NN
10_1101-436634	799	9	event	event	NN
10_1101-436634	799	10	with	with	IN
10_1101-436634	799	11	8	8	CD
10_1101-436634	799	12	and	and	CC
10_1101-436634	799	13	6	6	CD
10_1101-436634	799	14	reads	read	NNS
10_1101-436634	799	15	of	of	IN
10_1101-436634	799	16	support	support	NN
10_1101-436634	799	17	for	for	IN
10_1101-436634	799	18	the	the	DT
10_1101-436634	799	19	samples	sample	NNS
10_1101-436634	799	20	shown	show	VBN
10_1101-436634	799	21	.	.	.
10_1101-436634	800	1	This	this	DT
10_1101-436634	800	2	result	result	NN
10_1101-436634	800	3	was	be	VBD
10_1101-436634	800	4	found	find	VBN
10_1101-436634	800	5	using	use	VBG
10_1101-436634	800	6	the	the	DT
10_1101-436634	800	7	default	default	NN
10_1101-436634	800	8	splice	splice	NN
10_1101-436634	800	9	variant	variant	JJ
10_1101-436634	800	10	window	window	NN
10_1101-436634	800	11	parameter	parameter	NN
10_1101-436634	800	12	(	(	-LRB-
10_1101-436634	800	13	i2e3	i2e3	ADD
10_1101-436634	800	14	)	)	-RRB-
10_1101-436634	800	15	.	.	.
10_1101-436634	801	1	B	b	NN
10_1101-436634	801	2	)	)	-RRB-
10_1101-436634	801	3	Sashimi	Sashimi	NNP
10_1101-436634	801	4	plot	plot	NN
10_1101-436634	801	5	visualization	visualization	NN
10_1101-436634	801	6	of	of	IN
10_1101-436634	801	7	the	the	DT
10_1101-436634	801	8	novel	novel	JJ
10_1101-436634	801	9	junction	junction	NN
10_1101-436634	801	10	.	.	.
10_1101-436634	802	1	.CC	.CC	NFP
10_1101-436634	802	2	-	-	:
10_1101-436634	802	3	BY	by	IN
10_1101-436634	802	4	-	-	HYPH
10_1101-436634	802	5	NC	NC	NNP
10_1101-436634	802	6	-	-	HYPH
10_1101-436634	802	7	ND	ND	NNP
10_1101-436634	802	8	4.0	4.0	CD
10_1101-436634	802	9	International	international	JJ
10_1101-436634	802	10	licensea	licensea	NNS
10_1101-436634	802	11	certified	certify	VBN
10_1101-436634	802	12	by	by	IN
10_1101-436634	802	13	peer	peer	NN
10_1101-436634	802	14	review	review	NN
10_1101-436634	802	15	)	)	-RRB-
10_1101-436634	802	16	is	be	VBZ
10_1101-436634	802	17	the	the	DT
10_1101-436634	802	18	author	author	NN
10_1101-436634	802	19	/	/	SYM
10_1101-436634	802	20	funder	funder	NN
10_1101-436634	802	21	,	,	,
10_1101-436634	802	22	who	who	WP
10_1101-436634	802	23	has	have	VBZ
10_1101-436634	802	24	granted	grant	VBN
10_1101-436634	802	25	bioRxiv	biorxiv	IN
10_1101-436634	802	26	a	a	DT
10_1101-436634	802	27	license	license	NN
10_1101-436634	802	28	to	to	TO
10_1101-436634	802	29	display	display	VB
10_1101-436634	802	30	the	the	DT
10_1101-436634	802	31	preprint	preprint	NN
10_1101-436634	802	32	in	in	IN
10_1101-436634	802	33	perpetuity	perpetuity	NN
10_1101-436634	802	34	.	.	.
10_1101-436634	803	1	It	-PRON-	PRP
10_1101-436634	803	2	is	be	VBZ
10_1101-436634	803	3	made	make	VBN
10_1101-436634	803	4	available	available	JJ
10_1101-436634	803	5	under	under	IN
10_1101-436634	803	6	The	the	DT
10_1101-436634	803	7	copyright	copyright	NN
10_1101-436634	803	8	holder	holder	NN
10_1101-436634	803	9	for	for	IN
10_1101-436634	803	10	this	this	DT
10_1101-436634	803	11	preprint	preprint	NN
10_1101-436634	803	12	(	(	-LRB-
10_1101-436634	803	13	which	which	WDT
10_1101-436634	803	14	was	be	VBD
10_1101-436634	803	15	notthis	notthis	DT
10_1101-436634	803	16	version	version	NN
10_1101-436634	803	17	posted	post	VBN
10_1101-436634	803	18	January	January	NNP
10_1101-436634	803	19	5	5	CD
10_1101-436634	803	20	,	,	,
10_1101-436634	803	21	2021	2021	CD
10_1101-436634	803	22	.	.	.
10_1101-436634	803	23	;	;	:
10_1101-436634	803	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	803	25	:	:	:
10_1101-436634	803	26	bioRxiv	biorxiv	VB
10_1101-436634	803	27	preprint	preprint	NN
10_1101-436634	803	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	803	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	PDT
10_1101-436634	803	30	47	47	CD
10_1101-436634	803	31	.CC	.CC	NFP
10_1101-436634	803	32	-	-	HYPH
10_1101-436634	803	33	BY	by	IN
10_1101-436634	803	34	-	-	HYPH
10_1101-436634	803	35	NC	NC	NNP
10_1101-436634	803	36	-	-	HYPH
10_1101-436634	803	37	ND	ND	NNP
10_1101-436634	803	38	4.0	4.0	CD
10_1101-436634	803	39	International	international	JJ
10_1101-436634	803	40	licensea	licensea	NNS
10_1101-436634	803	41	certified	certify	VBN
10_1101-436634	803	42	by	by	IN
10_1101-436634	803	43	peer	peer	NN
10_1101-436634	803	44	review	review	NN
10_1101-436634	803	45	)	)	-RRB-
10_1101-436634	803	46	is	be	VBZ
10_1101-436634	803	47	the	the	DT
10_1101-436634	803	48	author	author	NN
10_1101-436634	803	49	/	/	SYM
10_1101-436634	803	50	funder	funder	NN
10_1101-436634	803	51	,	,	,
10_1101-436634	803	52	who	who	WP
10_1101-436634	803	53	has	have	VBZ
10_1101-436634	803	54	granted	grant	VBN
10_1101-436634	803	55	bioRxiv	biorxiv	IN
10_1101-436634	803	56	a	a	DT
10_1101-436634	803	57	license	license	NN
10_1101-436634	803	58	to	to	TO
10_1101-436634	803	59	display	display	VB
10_1101-436634	803	60	the	the	DT
10_1101-436634	803	61	preprint	preprint	NN
10_1101-436634	803	62	in	in	IN
10_1101-436634	803	63	perpetuity	perpetuity	NN
10_1101-436634	803	64	.	.	.
10_1101-436634	804	1	It	-PRON-	PRP
10_1101-436634	804	2	is	be	VBZ
10_1101-436634	804	3	made	make	VBN
10_1101-436634	804	4	available	available	JJ
10_1101-436634	804	5	under	under	IN
10_1101-436634	804	6	The	the	DT
10_1101-436634	804	7	copyright	copyright	NN
10_1101-436634	804	8	holder	holder	NN
10_1101-436634	804	9	for	for	IN
10_1101-436634	804	10	this	this	DT
10_1101-436634	804	11	preprint	preprint	NN
10_1101-436634	804	12	(	(	-LRB-
10_1101-436634	804	13	which	which	WDT
10_1101-436634	804	14	was	be	VBD
10_1101-436634	804	15	notthis	notthis	DT
10_1101-436634	804	16	version	version	NN
10_1101-436634	804	17	posted	post	VBN
10_1101-436634	804	18	January	January	NNP
10_1101-436634	804	19	5	5	CD
10_1101-436634	804	20	,	,	,
10_1101-436634	804	21	2021	2021	CD
10_1101-436634	804	22	.	.	.
10_1101-436634	804	23	;	;	:
10_1101-436634	804	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	804	25	:	:	:
10_1101-436634	804	26	bioRxiv	biorxiv	VB
10_1101-436634	804	27	preprint	preprint	NN
10_1101-436634	804	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	804	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	NFP
10_1101-436634	804	30	48	48	CD
10_1101-436634	804	31	Supplementary	Supplementary	NNP
10_1101-436634	804	32	Figure	Figure	NNP
10_1101-436634	804	33	14	14	CD
10_1101-436634	804	34	:	:	:
10_1101-436634	804	35	Several	several	JJ
10_1101-436634	804	36	SNVs	SNVs	NNPS
10_1101-436634	804	37	in	in	IN
10_1101-436634	804	38	CDKN2A	CDKN2A	NNP
10_1101-436634	804	39	associated	associate	VBN
10_1101-436634	804	40	with	with	IN
10_1101-436634	804	41	alternate	alternate	JJ
10_1101-436634	804	42	donor	donor	NN
10_1101-436634	804	43	usage	usage	NN
10_1101-436634	804	44	.	.	.
10_1101-436634	805	1	A	a	LS
10_1101-436634	805	2	)	)	-RRB-
10_1101-436634	805	3	IGV	igv	NN
10_1101-436634	805	4	snapshot	snapshot	NN
10_1101-436634	805	5	of	of	IN
10_1101-436634	805	6	three	three	CD
10_1101-436634	805	7	variant	variant	JJ
10_1101-436634	805	8	positions	position	NNS
10_1101-436634	805	9	in	in	IN
10_1101-436634	805	10	CDKN2A	CDKN2A	NNP
10_1101-436634	805	11	found	find	VBD
10_1101-436634	805	12	to	to	TO
10_1101-436634	805	13	be	be	VB
10_1101-436634	805	14	associated	associate	VBN
10_1101-436634	805	15	with	with	IN
10_1101-436634	805	16	usage	usage	NN
10_1101-436634	805	17	of	of	IN
10_1101-436634	805	18	an	an	DT
10_1101-436634	805	19	alternate	alternate	JJ
10_1101-436634	805	20	donor	donor	NN
10_1101-436634	805	21	site	site	NN
10_1101-436634	805	22	that	that	WDT
10_1101-436634	805	23	leads	lead	VBZ
10_1101-436634	805	24	to	to	IN
10_1101-436634	805	25	formation	formation	NN
10_1101-436634	805	26	of	of	IN
10_1101-436634	805	27	an	an	DT
10_1101-436634	805	28	alternate	alternate	JJ
10_1101-436634	805	29	known	know	VBN
10_1101-436634	805	30	transcript	transcript	NN
10_1101-436634	805	31	.	.	.
10_1101-436634	806	1	This	this	DT
10_1101-436634	806	2	result	result	NN
10_1101-436634	806	3	was	be	VBD
10_1101-436634	806	4	found	find	VBN
10_1101-436634	806	5	using	use	VBG
10_1101-436634	806	6	the	the	DT
10_1101-436634	806	7	default	default	NN
10_1101-436634	806	8	splice	splice	NN
10_1101-436634	806	9	variant	variant	JJ
10_1101-436634	806	10	window	window	NN
10_1101-436634	806	11	parameter	parameter	NN
10_1101-436634	806	12	(	(	-LRB-
10_1101-436634	806	13	i2e3	i2e3	ADD
10_1101-436634	806	14	)	)	-RRB-
10_1101-436634	806	15	for	for	IN
10_1101-436634	806	16	known	know	VBN
10_1101-436634	806	17	(	(	-LRB-
10_1101-436634	806	18	DA	DA	NNP
10_1101-436634	806	19	)	)	-RRB-
10_1101-436634	806	20	junctions	junction	NNS
10_1101-436634	806	21	.	.	.
10_1101-436634	807	1	B	b	NN
10_1101-436634	807	2	)	)	-RRB-
10_1101-436634	807	3	Zoomed	Zoomed	NNP
10_1101-436634	807	4	in	in	IN
10_1101-436634	807	5	view	view	NN
10_1101-436634	807	6	of	of	IN
10_1101-436634	807	7	the	the	DT
10_1101-436634	807	8	variants	variant	NNS
10_1101-436634	807	9	identified	identify	VBN
10_1101-436634	807	10	by	by	IN
10_1101-436634	807	11	RegTools	regtool	NNS
10_1101-436634	807	12	that	that	WDT
10_1101-436634	807	13	are	be	VBP
10_1101-436634	807	14	associated	associate	VBN
10_1101-436634	807	15	with	with	IN
10_1101-436634	807	16	alternate	alternate	JJ
10_1101-436634	807	17	donor	donor	NN
10_1101-436634	807	18	usage	usage	NN
10_1101-436634	807	19	.	.	.
10_1101-436634	808	1	Two	two	CD
10_1101-436634	808	2	of	of	IN
10_1101-436634	808	3	these	these	DT
10_1101-436634	808	4	variant	variant	JJ
10_1101-436634	808	5	positions	position	NNS
10_1101-436634	808	6	flank	flank	VBP
10_1101-436634	808	7	the	the	DT
10_1101-436634	808	8	donor	donor	NN
10_1101-436634	808	9	site	site	NN
10_1101-436634	808	10	that	that	WDT
10_1101-436634	808	11	is	be	VBZ
10_1101-436634	808	12	no	no	DT
10_1101-436634	808	13	longer	long	RBR
10_1101-436634	808	14	being	be	VBG
10_1101-436634	808	15	used	use	VBN
10_1101-436634	808	16	.	.	.
10_1101-436634	809	1	C	C	NNP
10_1101-436634	809	2	)	)	-RRB-
10_1101-436634	809	3	Sashimi	Sashimi	NNP
10_1101-436634	809	4	plot	plot	NN
10_1101-436634	809	5	visualizations	visualization	NNS
10_1101-436634	809	6	for	for	IN
10_1101-436634	809	7	samples	sample	NNS
10_1101-436634	809	8	containing	contain	VBG
10_1101-436634	809	9	the	the	DT
10_1101-436634	809	10	identified	identify	VBN
10_1101-436634	809	11	variants	variant	NNS
10_1101-436634	809	12	that	that	WDT
10_1101-436634	809	13	show	show	VBP
10_1101-436634	809	14	alternate	alternate	JJ
10_1101-436634	809	15	donor	donor	NN
10_1101-436634	809	16	usage	usage	NN
10_1101-436634	809	17	.	.	.
10_1101-436634	810	1	.CC	.CC	NFP
10_1101-436634	810	2	-	-	:
10_1101-436634	810	3	BY	by	IN
10_1101-436634	810	4	-	-	HYPH
10_1101-436634	810	5	NC	NC	NNP
10_1101-436634	810	6	-	-	HYPH
10_1101-436634	810	7	ND	ND	NNP
10_1101-436634	810	8	4.0	4.0	CD
10_1101-436634	810	9	International	international	JJ
10_1101-436634	810	10	licensea	licensea	NNS
10_1101-436634	810	11	certified	certify	VBN
10_1101-436634	810	12	by	by	IN
10_1101-436634	810	13	peer	peer	NN
10_1101-436634	810	14	review	review	NN
10_1101-436634	810	15	)	)	-RRB-
10_1101-436634	810	16	is	be	VBZ
10_1101-436634	810	17	the	the	DT
10_1101-436634	810	18	author	author	NN
10_1101-436634	810	19	/	/	SYM
10_1101-436634	810	20	funder	funder	NN
10_1101-436634	810	21	,	,	,
10_1101-436634	810	22	who	who	WP
10_1101-436634	810	23	has	have	VBZ
10_1101-436634	810	24	granted	grant	VBN
10_1101-436634	810	25	bioRxiv	biorxiv	IN
10_1101-436634	810	26	a	a	DT
10_1101-436634	810	27	license	license	NN
10_1101-436634	810	28	to	to	TO
10_1101-436634	810	29	display	display	VB
10_1101-436634	810	30	the	the	DT
10_1101-436634	810	31	preprint	preprint	NN
10_1101-436634	810	32	in	in	IN
10_1101-436634	810	33	perpetuity	perpetuity	NN
10_1101-436634	810	34	.	.	.
10_1101-436634	811	1	It	-PRON-	PRP
10_1101-436634	811	2	is	be	VBZ
10_1101-436634	811	3	made	make	VBN
10_1101-436634	811	4	available	available	JJ
10_1101-436634	811	5	under	under	IN
10_1101-436634	811	6	The	the	DT
10_1101-436634	811	7	copyright	copyright	NN
10_1101-436634	811	8	holder	holder	NN
10_1101-436634	811	9	for	for	IN
10_1101-436634	811	10	this	this	DT
10_1101-436634	811	11	preprint	preprint	NN
10_1101-436634	811	12	(	(	-LRB-
10_1101-436634	811	13	which	which	WDT
10_1101-436634	811	14	was	be	VBD
10_1101-436634	811	15	notthis	notthis	DT
10_1101-436634	811	16	version	version	NN
10_1101-436634	811	17	posted	post	VBN
10_1101-436634	811	18	January	January	NNP
10_1101-436634	811	19	5	5	CD
10_1101-436634	811	20	,	,	,
10_1101-436634	811	21	2021	2021	CD
10_1101-436634	811	22	.	.	.
10_1101-436634	811	23	;	;	:
10_1101-436634	811	24	https://doi.org/10.1101/436634doi	https://doi.org/10.1101/436634doi	NN
10_1101-436634	811	25	:	:	:
10_1101-436634	811	26	bioRxiv	biorxiv	VB
10_1101-436634	811	27	preprint	preprint	NN
10_1101-436634	811	28	https://doi.org/10.1101/436634	https://doi.org/10.1101/436634	NNP
10_1101-436634	811	29	http://creativecommons.org/licenses/by-nc-nd/4.0/	http://creativecommons.org/licenses/by-nc-nd/4.0/	RB