#INFO: PE => number of discordant paired end reads supporting the SV
#INFO: SR => number of split reads supporting the SV
#INFO: 1000G => 1000 Genomes Project call set
#INFO: DGV => Database of Genomic Variants
#INFO: GAP => UCSC gap regions
#INFO: inHouse => In-house database of SVs called in germline genomes
#INFO: COSMIC => COSMIC v86
#INFO: Cancer_census =>  Cancer Census COSMIC v86
#INFO: KnownFusion => Known list of fusions from NYGC and/or COSMIC
#chr1	start1	end1	chr2	start2	end2	type	score	strand1	strand2	evidence	tools	tumor--normal	info	cnv_changepoint_1	cnv_changepoint_2	splazerS_tumor	splazerS_normal
chrX	27188674	27188675	chrX	94069205	94069206	INV	NA	-	-	[Svaba_SR=36,Svaba_PE=28],[Manta_PE=28,Manta_SR=31],[Lumpy_PE=20,Lumpy_SR=22]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;gap;Cancer_census=ARAF,SSX1,WAS,FOXO4,ZMYM3,NONO,FAM47C,BCOR,DDX3X,SSX4,GATA1,TFE3,SSX2,SMC1A,AMER1,MSN,MED12,KDM5C,AR,KDM6A,RBM10,ATRX;DisruptL=AC107419.1;DisruptR=;ClosestL=AC112493.1;ClosestR=	27188582	94069001	28,27188673,94069204	0,0,0
chrX	77602700	77602701	chrX	77603722	77603723	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=32],[Manta_PE=23,Manta_SR=24],[Lumpy_PE=19,Lumpy_SR=17]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=ATRX;DisruptL=ATRX;DisruptR=ATRX;ClosestL=;ClosestR=	94069000	94069000	19,77602701,77603721	0,0,0
chrX	129340948	129340949	chrX	129372988	129372989	DUP	NA	-	+	[Svaba_SR=71,Svaba_PE=29],[Manta_PE=21,Manta_SR=38]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	123576327	123576327	47,129340950,129372990	0,0,0
chrX	154977661	154977662	chrX	154998320	154998321	DEL	NA	+	-	[Svaba_SR=62,Svaba_PE=90],[Manta_PE=79,Manta_SR=45],[Lumpy_PE=56,Lumpy_SR=39]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=F8;DisruptR=F8;ClosestL=;ClosestR=	156030795	156030795	38,154977662,154998319	0,0,0
chr1	11072158	11072159	chr19	37273781	37273782	TRA	NA	+	+	[Svaba_SR=35,Svaba_PE=26],[Manta_PE=12,Manta_SR=20]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=AL109811.1,EXOSC10;DisruptR=;ClosestL=SRM;ClosestR=AC016590.1	11071410	37270967	24,11072163,37273783	0,0,0
chr1	30938030	30938031	chr6	42280513	42280514	TRA	NA	-	+	[Svaba_SR=192,Svaba_PE=163],[Manta_PE=219,Manta_SR=171],[Lumpy_PE=173,Lumpy_SR=95]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=PUM1;DisruptR=TRERF1;Fusion=PUM1-TRERF1;ClosestL=RN7SL371P;ClosestR=	30937958	42280534	86,30938029,42280515	0,0,0
chr1	31088968	31088969	chr6	41330099	41330100	TRA	NA	+	-	[Svaba_SR=44,Svaba_PE=62],[Manta_PE=86,Manta_SR=81],[Lumpy_PE=63,Lumpy_SR=45]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;ClosestL=SELENOWP1;ClosestR=NCR2	31089319	41330046	18,31088970,41330090	0,0,0
chr1	37355319	37355320	chr1	37938872	37938873	DUP	NA	-	+	[Svaba_SR=40,Svaba_PE=41],[Manta_PE=36,Manta_SR=37],[Lumpy_PE=29,Lumpy_SR=22]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=INPP5B;ClosestL=;ClosestR=RF00017	31089320	31089320	29,37355319,37938874	0,0,0
chr1	63519740	63519741	chr1	63524915	63524916	INV	NA	-	-	[Svaba_SR=6,Svaba_PE=5],[Manta_PE=6,Manta_SR=4],[Lumpy_PE=4,Lumpy_SR=3]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=ITGB3BP;DisruptR=ITGB3BP,EFCAB7;Fusion=ITGB3BP+EFCAB7;ClosestL=EFCAB7;ClosestR=RN7SL488P	83995849	83995849	4,63519739,63524914	0,0,0
chr1	63523444	63523445	chr1	63825596	63825597	INV	NA	+	+	[Manta_PE=5,Manta_SR=5],[Lumpy_PE=3,Lumpy_SR=4]	lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=ITGB3BP,EFCAB7;DisruptR=ROR1;Fusion=ROR1+ITGB3BP;ClosestL=RN7SL488P;ClosestR=CFL1P3	83995849	83995849	4,63523446,63825598	0,0,0
chr1	79748086	79748087	chr1	79750126	79750127	DEL	NA	+	-	[Svaba_SR=28,Svaba_PE=47],[Manta_PE=39,Manta_SR=23],[Lumpy_PE=27,Lumpy_SR=20]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	83995849	83995849	19,79748085,79750125	0,0,0
chr1	83826732	83826733	chr8	99948485	99948486	TRA	NA	-	-	[Svaba_SR=19,Svaba_PE=20],[Manta_PE=20,Manta_SR=14],[Lumpy_PE=14,Lumpy_SR=6]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=LINC01725;DisruptR=;ClosestL=;ClosestR=RGS22	83995849	101318335	13,83826729,99948484	0,0,0
chr1	83995880	83995881	chr8	99977871	99977872	TRA	NA	+	+	[Svaba_SR=95,Svaba_PE=99],[Manta_PE=98,Manta_SR=87],[Lumpy_PE=56,Lumpy_SR=74]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=TTLL7;DisruptR=RGS22;ClosestL=TTLL7-IT1;ClosestR=	83995850	101318335	65,83995880,99977873	0,0,0
chr1	97547194	97547195	chrX	53249048	53249049	TRA	NA	+	+	[Svaba_SR=28,Svaba_PE=35],[Manta_PE=37,Manta_SR=24],[Lumpy_PE=24,Lumpy_SR=20]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=DPYD;DisruptR=IQSEC2;ClosestL=SEC63P1;ClosestR=	97547226	53249009	21,97547194,53249050	0,0,0
chr1	114927985	114927986	chr8	99977924	99977925	TRA	NA	-	-	[Svaba_SR=68,Svaba_PE=65],[Manta_PE=69,Manta_SR=58],[Lumpy_PE=50,Lumpy_SR=29]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=SYCP1;DisruptR=RGS22;Fusion=RGS22-SYCP1;ClosestL=;ClosestR=	114928001	101318335	49,114927987,99977923	0,0,0
chr1	115214766	115214767	chr1	115215649	115215650	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=71],[Manta_PE=43,Manta_SR=59],[Lumpy_PE=47,Lumpy_SR=38]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	114928002	114928002	37,115214760,115215642	0,0,0
chr1	117039408	117039409	chr1	117052486	117052487	INV	NA	-	-	[Svaba_SR=30,Svaba_PE=22],[Manta_PE=26,Manta_SR=25],[Lumpy_PE=15,Lumpy_SR=19]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=AL445231.1;DisruptR=AL445231.1;ClosestL=CD101;ClosestR=TTF2	117039360	117039360	22,117039409,117052485	0,0,0
chr1	145915224	145915225	chr1	145917334	145917335	DEL	NA	+	-	[Svaba_SR=64,Svaba_PE=65],[Manta_PE=56,Manta_SR=54],[Lumpy_PE=39,Lumpy_SR=23]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=PEX11B;DisruptR=PEX11B;ClosestL=RBM8A;ClosestR=RBM8A	143268055	143268055	43,145915224,145917333	0,0,0
chr1	152266457	152266458	chr1	152267969	152267970	DEL	NA	+	-	[Svaba_SR=67,Svaba_PE=92],[Manta_PE=64,Manta_SR=69]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=FLG-AS1;DisruptR=FLG-AS1;ClosestL=;ClosestR=	152269317	152269317	38,152266458,152268015	0,0,0
chr1	159123226	159123227	chr1	217446485	217446486	INV	NA	+	+	[Svaba_SR=64,Svaba_PE=50],[Manta_PE=48,Manta_SR=57],[Lumpy_PE=87,Lumpy_SR=94]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SLC45A3,FCGR2B,DDR2,PRRX1,ABL2,TPR,ELF3,MDM4,ELK4,SDHC,CDC73,PTPRC,PBX1;DisruptL=AIM2;DisruptR=GPATCH2;ClosestL=;ClosestR=	152269318	248946322	41,159123227,217446493	0,0,0
chr1	159123235	159123236	chr1	217446515	217446516	INV	NA	-	-	[Svaba_SR=63,Svaba_PE=67],[Manta_PE=65,Manta_SR=62],[Lumpy_PE=87,Lumpy_SR=94]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SLC45A3,FCGR2B,DDR2,PRRX1,ABL2,TPR,ELF3,MDM4,ELK4,SDHC,CDC73,PTPRC,PBX1;DisruptL=AIM2;DisruptR=GPATCH2;ClosestL=;ClosestR=	152269318	248946322	41,159123235,217446512	0,0,0
chr1	188818138	188818139	chr1	188819642	188819643	DEL	NA	+	-	[Svaba_SR=27,Svaba_PE=38],[Manta_PE=36,Manta_SR=21],[Lumpy_PE=27,Lumpy_SR=16]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	152269318	152269318	20,188818138,188819641	0,0,0
chr1	192351688	192351689	chr1	192488644	192488645	DUP	NA	-	+	[Svaba_SR=42,Svaba_PE=40],[Manta_PE=30,Manta_SR=40],[Lumpy_PE=22,Lumpy_SR=27]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=RGS21,AL390957.1;DisruptR=AL390957.1;ClosestL=;ClosestR=	152269318	152269318	31,192351692,192488646	0,0,0
chr1	229392453	229392454	chr1	230257952	230257953	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=14],[Manta_PE=14,Manta_SR=46]	manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=GALNT2;ClosestL=RNU6-180P;ClosestR=AL136988.2	248946322	248946322	8,229392477,230257952	0,0,0
chr1	229392621	229392622	chr1	230258179	230258180	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=28],[Manta_PE=28,Manta_SR=30]	manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=GALNT2;ClosestL=RNU6-180P;ClosestR=AL136988.2	248946322	248946322	7,229392643,230258122	0,0,0
chr2	1010782	1010783	chr2	1021396	1021397	DEL	NA	+	-	[Svaba_SR=35,Svaba_PE=33],[Manta_PE=29,Manta_SR=29],[Lumpy_PE=21,Lumpy_SR=16]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=SNTG2;DisruptR=SNTG2;ClosestL=;ClosestR=	10005	10005	19,1010788,1021395	0,0,0
chr2	10097680	10097681	chr2	10182038	10182039	DUP	NA	-	+	[Svaba_SR=71,Svaba_PE=74],[Manta_PE=57,Manta_SR=65],[Lumpy_PE=43,Lumpy_SR=47]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=AC007240.1,C2orf48;ClosestL=RF00568;ClosestR=MIR4261	11340510	11340510	49,10097679,10182040	0,0,0
chr2	11340628	11340629	chr2	55078510	55078511	DEL	NA	+	-	[Svaba_SR=25,Svaba_PE=38],[Manta_PE=32,Manta_SR=20],[Lumpy_PE=24,Lumpy_SR=15]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;gap;Cancer_census=MYCN,C2orf44,NCOA1,ASXL2,SIX2,EPAS1,MSH6,FBXO11,DNMT3A,STRN,EML4,MSH2,ALK,BIRC6;DisruptL=ROCK2;DisruptR=RTN4;Fusion=RTN4+ROCK2;ClosestL=PPIAP60;ClosestR=	11340511	55078447	17,11340627,55078509	0,0,0
chr2	19255709	19255710	chr2	19259885	19259886	INV	NA	+	+	[Svaba_SR=28,Svaba_PE=35],[Manta_PE=31,Manta_SR=25],[Lumpy_PE=38,Lumpy_SR=4]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=LINC01376;DisruptR=LINC01376;ClosestL=;ClosestR=	11340511	11340511	22,19255711,19259895	0,0,0
chr2	19255718	19255719	chr2	19260148	19260149	INV	NA	-	-	[Svaba_SR=23,Svaba_PE=9],[Manta_PE=12,Manta_SR=20],[Lumpy_PE=38,Lumpy_SR=4]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=LINC01376;DisruptR=LINC01376;ClosestL=;ClosestR=	11340511	11340511	0,0,0	0,0,0
chr2	22295031	22295032	chr2	22295565	22295566	DEL	NA	+	-	[Manta_PE=16,Manta_SR=14],[Lumpy_PE=6,Lumpy_SR=11]	lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=LINC01830;DisruptR=LINC01830;ClosestL=;ClosestR=	32953080	32953080	12,22295033,22295563	0,0,0
chr2	32953102	32953103	chr2	33018183	33018184	DEL	NA	+	-	[Svaba_SR=55,Svaba_PE=61],[Manta_PE=66,Manta_SR=50],[Lumpy_PE=50,Lumpy_SR=42]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=LTBP1;DisruptR=LTBP1;ClosestL=RF00019;ClosestR=	32953081	33018158	41,32953101,33018182	0,0,0
chr2	42434317	42434318	chr2	42451731	42451732	INV	NA	+	+	[Svaba_SR=37,Svaba_PE=41],[Manta_PE=38,Manta_SR=33],[Lumpy_PE=34,Lumpy_SR=7]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=KCNG3;ClosestL=RF00612;ClosestR=RF00612	33018158	33018158	27,42434321,42451736	0,0,0
chr2	42438491	42438492	chr2	42452836	42452837	INV	NA	-	-	[Svaba_SR=33,Svaba_PE=32],[Manta_PE=35,Manta_SR=32],[Lumpy_PE=23,Lumpy_SR=20]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=KCNG3;ClosestL=RF00612;ClosestR=VDAC1P13	33018158	33018158	24,42438483,42452835	0,0,0
chr2	53970217	53970218	chr2	90381211	90381212	INV	NA	+	+	[Lumpy_PE=8,Lumpy_SR=6]	lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;gap;Cancer_census=PCBP1,BCL11A,REL,XPO1,DCTN1;DisruptL=PSME4;DisruptR=;ClosestL=ACYP2;ClosestR=AC233263.6	53970147	70131215	17,53970217,90381212	0,0,0
chr2	66780784	66780785	chr2	67038412	67038413	DEL	NA	+	-	[Svaba_SR=33,Svaba_PE=48],[Manta_PE=44,Manta_SR=32],[Lumpy_PE=34,Lumpy_SR=17]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=;ClosestL=;ClosestR=AC007403.1	66780764	67038352	26,66780786,67038409	0,0,0
chr2	69932313	69932314	chr2	70131231	70131232	DEL	NA	+	-	[Svaba_SR=31,Svaba_PE=39],[Manta_PE=34,Manta_SR=31],[Lumpy_PE=24,Lumpy_SR=19]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=PCBP1;DisruptL=MXD1;DisruptR=;ClosestL=;ClosestR=LINC01816	69932250	70131215	23,69932315,70131220	0,0,0
chr2	78163397	78163398	chr2	78164890	78164891	DEL	NA	+	-	[Svaba_SR=37,Svaba_PE=38],[Manta_PE=33,Manta_SR=34],[Lumpy_PE=18,Lumpy_SR=22]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	70131215	70131215	30,78163395,78164889	0,0,0
chr2	104950250	104950251	chr2	105274703	105274704	DUP	NA	-	+	[Svaba_SR=25,Svaba_PE=38],[Manta_PE=34,Manta_SR=22],[Lumpy_PE=29,Lumpy_SR=17]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=AC010884.1;DisruptR=TGFBRAP1;Fusion=AC010884.1+TGFBRAP1;ClosestL=;ClosestR=	70131215	70131215	19,104950254,105274705	0,0,0
chr2	136280036	136280037	chr2	138107692	138107693	DUP	NA	-	+	[Manta_PE=2,Manta_SR=4]	manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=LINC01832	165996671	165996671	4,136280036,138107694	0,0,0
chr2	139754838	139754839	chr2	139755905	139755906	DEL	NA	+	-	[Svaba_SR=31,Svaba_PE=32],[Manta_PE=20,Manta_SR=25],[Lumpy_PE=20,Lumpy_SR=17]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	165996671	165996671	22,139754840,139755903	0,0,0
chr2	165996707	165996708	chr2	166087685	166087686	DEL	NA	+	-	[Svaba_SR=76,Svaba_PE=84],[Manta_PE=67,Manta_SR=59],[Lumpy_PE=50,Lumpy_SR=41]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=AC010127.1,SCN1A;DisruptR=AC010127.1,SCN1A;ClosestL=;ClosestR=	165996672	166087602	44,165996709,166087684	0,0,0
chr2	172150939	172150940	chr2	172227309	172227310	DUP	NA	-	+	[Svaba_SR=33,Svaba_PE=36],[Manta_PE=31,Manta_SR=31],[Lumpy_PE=27,Lumpy_SR=25]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	166087602	166087602	27,172150939,172227311	0,0,0
chr2	216347781	216347782	chr2	216348697	216348698	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=87],[Manta_PE=56,Manta_SR=63],[Lumpy_PE=48,Lumpy_SR=45]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=MARCH4;DisruptR=MARCH4;ClosestL=RF00019;ClosestR=RF00019	221633776	221633776	46,216347781,216348697	0,0,0
chr2	221633792	221633793	chr2	222290638	222290639	DUP	NA	-	+	[Svaba_SR=27,Svaba_PE=38],[Manta_PE=36,Manta_SR=23],[Lumpy_PE=28,Lumpy_SR=21]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=PAX3;DisruptL=;DisruptR=PAX3;ClosestL=AC068489.1;ClosestR=CCDC140	221633777	222260576	20,221633793,222290640	0,0,0
chr2	239473113	239473114	chr2	239518898	239518899	DUP	NA	-	+	[Svaba_SR=45,Svaba_PE=53],[Manta_PE=35,Manta_SR=39],[Lumpy_PE=30,Lumpy_SR=34]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;ClosestL=;ClosestR=	242183395	242183395	34,239473115,239518900	0,0,0
chr3	9464893	9464894	chr3	10566006	10566007	DUP	NA	-	+	[Svaba_SR=26,Svaba_PE=27],[Manta_PE=22,Manta_SR=23],[Lumpy_PE=19,Lumpy_SR=19]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=VHL,FANCD2;DisruptL=SETD5;DisruptR=ATP2B2;ClosestL=;ClosestR=ATP2B2-IT1	9464868	10565856	21,9464892,10566008	0,0,0
chr3	49398237	49398238	chr3	49547607	49547608	DUP	NA	-	+	[Svaba_SR=33,Svaba_PE=37],[Manta_PE=33,Manta_SR=27],[Lumpy_PE=28,Lumpy_SR=17]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=RHOA;DisruptR=;ClosestL=TCTA;ClosestR=BSN-DT	57140872	57140872	18,49398238,49547609	0,0,0
chr3	56435398	56435399	chr3	56440738	56440739	DUP	NA	-	+	[Svaba_SR=57,Svaba_PE=56],[Manta_PE=49,Manta_SR=46],[Lumpy_PE=44,Lumpy_SR=30]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=ERC2;DisruptR=ERC2;ClosestL=;ClosestR=	57140872	57140872	36,56435399,56440740	0,0,0
chr3	57140943	57140944	chr3	57246774	57246775	DUP	NA	-	+	[Svaba_SR=77,Svaba_PE=77],[Manta_PE=69,Manta_SR=67],[Lumpy_PE=62,Lumpy_SR=48]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=IL17RD;DisruptR=APPL1;ClosestL=AC097358.1;ClosestR=	57140873	57246746	46,57140944,57246776	0,0,0
chr3	129573007	129573008	chr3	129701071	129701072	DUP	NA	-	+	[Svaba_SR=44,Svaba_PE=55],[Manta_PE=49,Manta_SR=37],[Lumpy_PE=44,Lumpy_SR=27]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=PLXND1;DisruptR=TMCC1;Fusion=PLXND1+TMCC1;ClosestL=RN7SL752P;ClosestR=	129572683	129700972	32,129573010,129701073	0,0,0
chr3	134620707	134620708	chr3	134621343	134621344	DEL	NA	+	-	[Manta_PE=38,Manta_SR=63],[Lumpy_PE=36,Lumpy_SR=49]	manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=EPHB1,KY;DisruptR=EPHB1,KY;ClosestL=;ClosestR=	129700972	129700972	44,134620709,134621343	0,0,0
chr3	155419720	155419721	chr3	155430641	155430642	DEL	NA	+	-	[Svaba_SR=69,Svaba_PE=75],[Manta_PE=67,Manta_SR=52],[Lumpy_PE=49,Lumpy_SR=40]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=PLCH1;DisruptR=PLCH1;ClosestL=AC108729.1;ClosestR=AC108729.1	129700972	129700972	41,155419721,155430640	0,0,0
chr4	13433848	13433849	chr4	13867779	13867780	DUP	NA	-	+	[Svaba_SR=31,Svaba_PE=38],[Manta_PE=32,Manta_SR=26],[Lumpy_PE=29,Lumpy_SR=22]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=RAB28;DisruptR=LINC01182;ClosestL=;ClosestR=	13433767	13867712	21,13433848,13867781	0,0,0
chr4	15623654	15623655	chr4	15715678	15715679	DUP	NA	-	+	[Svaba_SR=30,Svaba_PE=36],[Manta_PE=33,Manta_SR=25],[Lumpy_PE=28,Lumpy_SR=19]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=FBXL5;DisruptR=BST1;ClosestL=;ClosestR=FAM200B	13867712	13867712	21,15623654,15715680	0,0,0
chr4	40767408	40767409	chr4	40818586	40818587	DUP	NA	-	+	[Svaba_SR=61,Svaba_PE=62],[Manta_PE=34,Manta_SR=51]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=NSUN7;DisruptR=AC131953.1,APBB2;Fusion=AC131953.1+NSUN7;ClosestL=ARL4AP2;ClosestR=RF00019	13867712	13867712	40,40767410,40818588	0,0,0
chr4	42401409	42401410	chr4	42405144	42405145	DEL	NA	+	-	[Svaba_SR=48,Svaba_PE=52],[Manta_PE=46,Manta_SR=44],[Lumpy_PE=26,Lumpy_SR=33]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=SHISA3;DisruptR=;ClosestL=ATP8A1;ClosestR=SHISA3	13867712	13867712	28,42401416,42405143	0,0,0
chr4	78063526	78063527	chr4	78098602	78098603	DUP	NA	-	+	[Svaba_SR=63,Svaba_PE=57],[Manta_PE=49,Manta_SR=58],[Lumpy_PE=42,Lumpy_SR=35]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=FRAS1;DisruptR=FRAS1;ClosestL=;ClosestR=	136871289	136871289	32,78063516,78098604	0,0,0
chr4	81355261	81355262	chr4	81461460	81461461	DUP	NA	-	+	[Svaba_SR=30,Svaba_PE=31],[Manta_PE=23,Manta_SR=26],[Lumpy_PE=18,Lumpy_SR=23]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=RASGEF1B;ClosestL=;ClosestR=	136871289	136871289	23,81355263,81461462	0,0,0
chr4	90900818	90900819	chr4	90936440	90936441	DUP	NA	-	+	[Svaba_SR=42,Svaba_PE=63],[Manta_PE=60,Manta_SR=36],[Lumpy_PE=55,Lumpy_SR=16]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=CCSER1;DisruptR=CCSER1;ClosestL=;ClosestR=	136871289	136871289	27,90900819,90936442	0,0,0
chr4	112106845	112106846	chr4	112180052	112180053	DEL	NA	+	-	[Svaba_SR=3,Svaba_PE=3],[Lumpy_PE=2,Lumpy_SR=2]	lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=FAM241A;ClosestL=AC093663.1;ClosestR=AC093663.2	136871289	136871289	3,112106847,112180050	0,0,0
chr4	116456576	116456577	chr4	116469025	116469026	DUP	NA	-	+	[Svaba_SR=30,Svaba_PE=30],[Manta_PE=22,Manta_SR=29],[Lumpy_PE=21,Lumpy_SR=21]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;ClosestL=;ClosestR=	136871289	136871289	25,116456575,116469029	0,0,0
chr4	136871281	136871282	chr4	136898160	136898161	DEL	NA	+	-	[Svaba_SR=65,Svaba_PE=80],[Manta_PE=78,Manta_SR=55],[Lumpy_PE=55,Lumpy_SR=24]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=LINC02511;DisruptR=LINC02511;ClosestL=;ClosestR=	136871289	136898090	15,136871279,136898159	0,0,0
chr4	145157655	145157656	chr4	145585044	145585045	DUP	NA	-	+	[Svaba_SR=57,Svaba_PE=67],[Manta_PE=62,Manta_SR=53],[Lumpy_PE=61,Lumpy_SR=15]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=OTUD4;DisruptR=;ClosestL=RF00019;ClosestR=LINC02491	145157668	145584969	28,145157654,145585047	0,0,0
chr4	172008972	172008973	chr4	172009701	172009702	DEL	NA	+	-	[Svaba_SR=33,Svaba_PE=30],[Manta_PE=25,Manta_SR=30],[Lumpy_PE=20,Lumpy_SR=19]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=GALNTL6;DisruptR=GALNTL6;ClosestL=;ClosestR=	190066290	190066290	24,172008974,172009696	0,0,0
chr5	1300944	1300945	chr5	1341135	1341136	DEL	NA	+	-	[Svaba_SR=34,Svaba_PE=54],[Manta_PE=46,Manta_SR=26],[Lumpy_PE=38,Lumpy_SR=19]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=CLPTM1L;ClosestL=TERT;ClosestR=	11484	11484	24,1300946,1341133	0,0,0
chr5	35556288	35556289	chr5	35558777	35558778	DEL	NA	+	-	[Svaba_SR=70,Svaba_PE=75],[Manta_PE=70,Manta_SR=60],[Lumpy_PE=43,Lumpy_SR=45]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	46492487	46492487	45,35556294,35558775	0,0,0
chr5	37047378	37047379	chr5	37139698	37139699	DUP	NA	-	+	[Svaba_SR=31,Svaba_PE=35],[Manta_PE=35,Manta_SR=27],[Lumpy_PE=31,Lumpy_SR=16]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=NIPBL;DisruptR=CPLANE1;ClosestL=;ClosestR=C8orf59P2	46492487	46492487	22,37047378,37139700	0,0,0
chr5	66379919	66379920	chr5	66401392	66401393	DUP	NA	-	+	[Svaba_SR=46,Svaba_PE=47],[Manta_PE=45,Manta_SR=38],[Lumpy_PE=36,Lumpy_SR=22]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	46492488	46492488	30,66379919,66401394	0,0,0
chr5	103966799	103966800	chr6	160114953	160114954	TRA	NA	+	-	[Manta_PE=0,Manta_SR=61]	manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=IGF2R	46492488	149656201	33,103966801,160114952	0,0,0
chr5	175048147	175048148	chr5	175109272	175109273	DUP	NA	-	+	[Svaba_SR=30,Svaba_PE=35],[Manta_PE=27,Manta_SR=24],[Lumpy_PE=23,Lumpy_SR=20]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;ClosestL=;ClosestR=	181449255	181449255	22,175048148,175109274	0,0,0
chr6	1719768	1719769	chr6	5740662	5740663	DEL	NA	+	-	[Svaba_SR=31,Svaba_PE=32],[Manta_PE=30,Manta_SR=30],[Lumpy_PE=20,Lumpy_SR=16]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=GMDS;DisruptR=FARS2;ClosestL=;ClosestR=	1864356	5740656	0,0,0	0,0,0
chr6	1809635	1809636	chr6	1864313	1864314	DUP	NA	-	+	[Svaba_SR=67,Svaba_PE=81],[Manta_PE=72,Manta_SR=61],[Lumpy_PE=56,Lumpy_SR=51]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=GMDS;DisruptR=GMDS;ClosestL=;ClosestR=	1864356	1864356	49,1809636,1864315	0,0,0
chr6	2101212	2101213	chr6	2119073	2119074	DUP	NA	-	+	[Svaba_SR=26,Svaba_PE=35],[Manta_PE=30,Manta_SR=23],[Lumpy_PE=26,Lumpy_SR=17]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=GMDS;DisruptR=GMDS;ClosestL=;ClosestR=	1864357	1864357	22,2101213,2119075	0,0,0
chr6	11282995	11282996	chr6	11465415	11465416	DUP	NA	-	+	[Svaba_SR=42,Svaba_PE=47],[Manta_PE=45,Manta_SR=40],[Lumpy_PE=33,Lumpy_SR=30]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=NEDD9;DisruptR=AL445430.1;ClosestL=;ClosestR=	5740656	5740656	31,11282995,11465417	0,0,0
chr6	13191208	13191209	chr18	4779517	4779518	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=23],[Manta_PE=23,Manta_SR=0]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=PHACTR1;DisruptR=AP005203.1;Fusion=PHACTR1-AP005203.1;ClosestL=;ClosestR=	5740656	8939025	0,0,0	0,0,0
chr6	32646348	32646349	chr15	41602686	41602687	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=8],[Manta_PE=8,Manta_SR=0]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=HLA-DQA1;DisruptR=;ClosestL=HLA-DQB1;ClosestR=AC016134.1	41330045	34526120	0,0,0	0,0,0
chr6	38868675	38868676	chr6	38961594	38961595	DUP	NA	-	+	[Svaba_SR=21,Svaba_PE=32],[Manta_PE=27,Manta_SR=22],[Lumpy_PE=19,Lumpy_SR=16]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=DNAH8;DisruptR=DNAH8;ClosestL=;ClosestR=AL034345.2	41330045	41330045	20,38868675,38961596	0,0,0
chr6	41234532	41234533	chr6	41719688	41719689	DUP	NA	-	+	[Svaba_SR=24,Svaba_PE=34],[Manta_PE=29,Manta_SR=23],[Lumpy_PE=27,Lumpy_SR=16]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=TFEB;DisruptL=TREML4;DisruptR=TFEB;ClosestL=RNA5SP207;ClosestR=AL035588.1	41330045	41330046	21,41234532,41719690	0,0,0
chr6	41400802	41400803	chr6	41494575	41494576	DUP	NA	-	+	[Svaba_SR=62,Svaba_PE=73],[Manta_PE=63,Manta_SR=57],[Lumpy_PE=53,Lumpy_SR=43]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=;ClosestL=AL136967.2;ClosestR=FOXP4-AS1	41330046	41330046	42,41400801,41494579	0,0,0
chr6	100490954	100490955	chr6	100700604	100700605	DEL	NA	+	-	[Svaba_SR=37,Svaba_PE=51],[Manta_PE=40,Manta_SR=31],[Lumpy_PE=27,Lumpy_SR=26]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=ASCC3;ClosestL=ASCC3;ClosestR=	78326602	78326602	27,100490955,100700603	0,0,0
chr6	134006352	134006353	chr6	134216603	134216604	DEL	NA	+	-	[Svaba_SR=76,Svaba_PE=81],[Manta_PE=71,Manta_SR=63],[Lumpy_PE=51,Lumpy_SR=43]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SGK1;DisruptL=SLC2A12;DisruptR=SGK1;Fusion=SGK1+SLC2A12;ClosestL=AL449363.1;ClosestR=RPS29P32	134006348	134216593	46,134006354,134216602	0,0,0
chr6	149186418	149186419	chr6	149655862	149655863	DUP	NA	-	+	[Svaba_SR=33,Svaba_PE=41],[Manta_PE=35,Manta_SR=24],[Lumpy_PE=33,Lumpy_SR=14]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=;ClosestL=;ClosestR=LATS1	149186362	149656200	19,149186420,149655864	0,0,0
chr7	56125408	56125409	chr7	56125919	56125920	DEL	NA	+	-	[Svaba_SR=30,Svaba_PE=31],[Manta_PE=21,Manta_SR=27],[Lumpy_PE=5,Lumpy_SR=13]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=NUPR2;ClosestR=NUPR2	16339	16339	19,56125414,56125918	0,0,0
chr7	70495123	70495124	chr7	70530566	70530567	DUP	NA	-	+	[Svaba_SR=31,Svaba_PE=31],[Manta_PE=30,Manta_SR=27],[Lumpy_PE=23,Lumpy_SR=23]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=AUTS2;DisruptR=AUTS2;ClosestL=;ClosestR=	16339	16339	19,70495128,70530568	0,0,0
chr7	73486322	73486323	chr7	73690169	73690170	DUP	NA	-	+	[Manta_PE=40,Manta_SR=16],[Lumpy_PE=39,Lumpy_SR=6]	lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=BAZ1B;DisruptR=BUD23;ClosestL=;ClosestR=DNAJC30	16339	16339	16,73486327,73690176	0,0,0
chr7	104903199	104903200	chr7	105089002	105089003	DUP	NA	-	+	[Svaba_SR=21,Svaba_PE=21],[Manta_PE=18,Manta_SR=17],[Lumpy_PE=12,Lumpy_SR=13]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=LHFPL3-AS2,LHFPL3;DisruptR=KMT2E;Fusion=KMT2E+LHFPL3;ClosestL=RN7SL8P;ClosestR=AC005070.3	149535564	149535564	16,104903200,105089004	0,0,0
chr7	111418017	111418018	chr7	111440360	111440361	DEL	NA	+	-	[Svaba_SR=57,Svaba_PE=65],[Manta_PE=62,Manta_SR=47],[Lumpy_PE=44,Lumpy_SR=32]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=IMMP2L;DisruptR=IMMP2L;ClosestL=AC003989.1;ClosestR=	149535564	149535564	37,111418018,111440359	0,0,0
chr7	133451388	133451389	chr7	133535567	133535568	DEL	NA	+	-	[Svaba_SR=67,Svaba_PE=76],[Manta_PE=67,Manta_SR=59],[Lumpy_PE=37,Lumpy_SR=50]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=EXOC4;DisruptR=EXOC4;ClosestL=;ClosestR=	149535564	149535564	43,133451390,133535566	0,0,0
chr7	148080561	148080562	chr7	148086389	148086390	DUP	NA	-	+	[Svaba_SR=29,Svaba_PE=28],[Manta_PE=29,Manta_SR=23],[Lumpy_PE=29,Lumpy_SR=3]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=CNTNAP2;DisruptL=CNTNAP2;DisruptR=CNTNAP2;ClosestL=;ClosestR=	149535564	149535564	13,148080560,148086391	0,0,0
chr7	149545776	149545777	chr8	142901156	142901157	TRA	NA	+	-	[Svaba_SR=47,Svaba_PE=57],[Manta_PE=55,Manta_SR=46],[Lumpy_PE=37,Lumpy_SR=32]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=GML;ClosestL=ZNF767P;ClosestR=CYP11B2	149535565	142901154	30,149545777,142901155	0,0,0
chr8	6065794	6065795	chr8	6141974	6141975	DUP	NA	-	+	[Svaba_SR=27,Svaba_PE=41],[Manta_PE=34,Manta_SR=23],[Lumpy_PE=29,Lumpy_SR=21]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=AC009435.1;DisruptR=AC009435.1;ClosestL=;ClosestR=	71162	71162	20,6065797,6141976	0,0,0
chr8	6635783	6635784	chr8	6742182	6742183	DUP	NA	-	+	[Svaba_SR=33,Svaba_PE=46],[Manta_PE=41,Manta_SR=28],[Lumpy_PE=36,Lumpy_SR=23]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=MCPH1,MCPH1-AS1;DisruptR=AGPAT5;Fusion=AGPAT5+MCPH1;ClosestL=MIR8055;ClosestR=MIR4659A	71162	71162	24,6635787,6742184	0,0,0
chr8	18290510	18290511	chr8	18291372	18291373	DEL	NA	+	-	[Svaba_SR=36,Svaba_PE=48],[Manta_PE=23,Manta_SR=32],[Lumpy_PE=24,Lumpy_SR=27]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	71162	71162	26,18290511,18291371	0,0,0
chr8	41600317	41600318	chr8	41611794	41611795	DEL	NA	+	-	[Svaba_SR=57,Svaba_PE=62],[Manta_PE=55,Manta_SR=44],[Lumpy_PE=36,Lumpy_SR=29]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=GPAT4;DisruptR=GPAT4,AC009630.3;ClosestL=AC009630.3;ClosestR=	71162	71162	34,41600315,41611793	0,0,0
chr8	47515973	47515974	chr8	47553070	47553071	DUP	NA	-	+	[Svaba_SR=31,Svaba_PE=44],[Manta_PE=39,Manta_SR=25],[Lumpy_PE=36,Lumpy_SR=2]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=SPIDR;DisruptR=SPIDR;ClosestL=AC024451.2;ClosestR=AC024451.1	71162	71162	22,47515975,47553072	0,0,0
chr8	52066260	52066261	chr8	52081342	52081343	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=36],[Manta_PE=29,Manta_SR=19],[Lumpy_PE=16,Lumpy_SR=18]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	101318335	101318335	16,52066261,52081341	0,0,0
chr8	53957268	53957269	chr8	54114333	54114334	DUP	NA	-	+	[Svaba_SR=37,Svaba_PE=41],[Manta_PE=41,Manta_SR=30],[Lumpy_PE=32,Lumpy_SR=21]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=TCEA1;DisruptL=RGS20;DisruptR=;ClosestL=TCEA1;ClosestR=LYPLA1	101318335	101318335	25,53957267,54114335	0,0,0
chr8	69198197	69198198	chr8	69202920	69202921	DEL	NA	+	-	[Svaba_SR=38,Svaba_PE=37],[Manta_PE=30,Manta_SR=33],[Lumpy_PE=17,Lumpy_SR=28]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;ClosestL=;ClosestR=	101318335	101318335	30,69198197,69202919	0,0,0
chr8	78849924	78849925	chr8	78875721	78875722	DUP	NA	-	+	[Svaba_SR=31,Svaba_PE=34],[Manta_PE=31,Manta_SR=22],[Lumpy_PE=25,Lumpy_SR=20]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;ClosestL=AC083837.1;ClosestR=	101318335	101318335	20,78849924,78875723	0,0,0
chr8	101318365	101318366	chr8	101478031	101478032	DUP	NA	-	+	[Svaba_SR=65,Svaba_PE=87],[Manta_PE=80,Manta_SR=48],[Lumpy_PE=70,Lumpy_SR=42]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=AP001207.3;ClosestL=RNU7-67P;ClosestR=GRHL2	101318336	101478031	26,101318367,101478033	0,0,0
chr8	107973150	107973151	chr8	107974357	107974358	DEL	NA	+	-	[Svaba_SR=23,Svaba_PE=44],[Manta_PE=32,Manta_SR=26],[Lumpy_PE=40,Lumpy_SR=7]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=RSPO2;DisruptL=RSPO2;DisruptR=RSPO2;ClosestL=NRBF2P4;ClosestR=NRBF2P4	101478032	101478032	22,107973141,107974381	0,0,0
chr8	123656928	123656929	chr8	126449890	126449891	DEL	NA	+	-	[Svaba_SR=70,Svaba_PE=85],[Manta_PE=71,Manta_SR=63],[Lumpy_PE=52,Lumpy_SR=36]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=AC090193.1;DisruptR=;ClosestL=KLHL38;ClosestR=	123656901	126449872	44,123656930,126449889	0,0,0
chr9	12889268	12889269	chr9	13056053	13056054	DUP	NA	-	+	[Svaba_SR=97,Svaba_PE=129],[Manta_PE=116,Manta_SR=83],[Lumpy_PE=94,Lumpy_SR=64]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=;ClosestL=RF00019;ClosestR=	12889209	13056040	3,12889266,13056059	0,0,0
chr9	27320055	27320056	chr9	27369387	27369388	DUP	NA	-	+	[Svaba_SR=38,Svaba_PE=48],[Manta_PE=48,Manta_SR=33],[Lumpy_PE=40,Lumpy_SR=16]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=MOB3B;ClosestL=MOB3B;ClosestR=	13056040	13056040	29,27320056,27369389	0,0,0
chr9	65206144	65206145	chr9	65815487	65815488	INV	NA	+	+	[Svaba_SR=0,Svaba_PE=8],[Manta_PE=7,Manta_SR=0]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;gap;DisruptL=;DisruptR=;ClosestL=BMS1P12;ClosestR=BX284632.1	112114443	112114443	0,0,0	0,0,0
chr9	100401327	100401328	chr9	100463898	100463899	DUP	NA	-	+	[Svaba_SR=26,Svaba_PE=39],[Manta_PE=35,Manta_SR=23],[Lumpy_PE=30,Lumpy_SR=21]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=MSANTD3-TMEFF1;ClosestL=;ClosestR=TMEFF1	112114443	112114443	20,100401333,100463900	0,0,0
chr9	112114499	112114500	chr9	112332630	112332631	DUP	NA	-	+	[Svaba_SR=76,Svaba_PE=88],[Manta_PE=77,Manta_SR=68],[Lumpy_PE=69,Lumpy_SR=46]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=SUSD1;DisruptR=PTBP3;Fusion=SUSD1+PTBP3;ClosestL=;ClosestR=	112114444	112332601	50,112114502,112332632	0,0,0
chr9	128994609	128994610	chr9	129001531	129001532	DUP	NA	-	+	[Svaba_SR=107,Svaba_PE=119],[Manta_PE=108,Manta_SR=90],[Lumpy_PE=90,Lumpy_SR=67]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=NUP188;DisruptR=NUP188;ClosestL=AL592211.1;ClosestR=AL592211.1	138313848	138313848	62,128994611,129001533	0,0,0
chr10	1138254	1138255	chr10	1549146	1549147	DEL	NA	+	-	[Svaba_SR=37,Svaba_PE=77],[Manta_PE=64,Manta_SR=29],[Lumpy_PE=57,Lumpy_SR=24]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=ADARB2-AS1,ADARB2;ClosestL=WDR37;ClosestR=	1138118	1549131	3,1138253,1549145	0,0,0
chr10	14534638	14534639	chr10	14566897	14566898	DEL	NA	+	-	[Svaba_SR=107,Svaba_PE=128],[Manta_PE=111,Manta_SR=82]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=FAM107B;DisruptR=FAM107B;ClosestL=;ClosestR=	22502452	22502452	60,14534635,14566896	0,0,0
chr10	22502966	22502967	chr13	58800117	58800118	TRA	NA	+	+	[Svaba_SR=88,Svaba_PE=82],[Manta_PE=88,Manta_SR=84],[Lumpy_PE=78,Lumpy_SR=91]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;ClosestL=;ClosestR=	22502453	58800227	57,22502966,58800119	0,0,0
chr10	22503061	22503062	chr13	58800154	58800155	TRA	NA	-	-	[Svaba_SR=22,Svaba_PE=39],[Manta_PE=37,Manta_SR=18]	manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;ClosestL=;ClosestR=	22502453	58800227	5,22503062,58800153	0,0,0
chr10	29842811	29842812	chr10	30116446	30116447	DUP	NA	-	+	[Svaba_SR=26,Svaba_PE=35],[Manta_PE=30,Manta_SR=22],[Lumpy_PE=24,Lumpy_SR=20]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=JCAD	22502453	22502453	21,29842813,30116448	0,0,0
chr10	48536424	48536425	chr10	48844584	48844585	DUP	NA	-	+	[Manta_PE=2,Manta_SR=4]	manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=ARHGAP22;DisruptR=WDFY4;ClosestL=AC016397.1;ClosestR=	71741418	71741418	4,48536424,48844586	0,0,0
chr10	62245654	62245655	chr10	62246248	62246249	DEL	NA	+	-	[Manta_PE=25,Manta_SR=35],[Lumpy_PE=16,Lumpy_SR=30]	manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=RTKN2;DisruptR=RTKN2;ClosestL=;ClosestR=	71741418	71741418	31,62245656,62246248	0,0,0
chr10	71741183	71741184	chr19	50944475	50944476	TRA	NA	-	-	[Svaba_SR=36,Svaba_PE=28],[Manta_PE=23,Manta_SR=33],[Lumpy_PE=16,Lumpy_SR=25]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=CDH23;DisruptR=KLK5;Fusion=KLK5-CDH23;ClosestL=C10orf105;ClosestR=AC011483.2	71741418	50944419	27,71741183,50944474	0,0,0
chr10	72412803	72412804	chr10	72415253	72415254	DEL	NA	+	-	[Svaba_SR=37,Svaba_PE=38],[Manta_PE=32,Manta_SR=36],[Lumpy_PE=23,Lumpy_SR=14]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=MICU1;DisruptR=MICU1;ClosestL=;ClosestR=	71741419	71741419	30,72412802,72415252	0,0,0
chr10	75984728	75984729	chr10	77999541	77999542	DEL	NA	+	-	[Svaba_SR=83,Svaba_PE=81],[Manta_PE=70,Manta_SR=73],[Lumpy_PE=41,Lumpy_SR=55]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=LRMDA;DisruptR=POLR3A;ClosestL=;ClosestR=	77999458	77999459	49,75984730,77999540	0,0,0
chr10	75985008	75985009	chr10	75986186	75986187	INV	NA	-	-	[Svaba_SR=29,Svaba_PE=38],[Manta_PE=35,Manta_SR=26],[Lumpy_PE=30,Lumpy_SR=19]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=LRMDA;DisruptR=LRMDA;ClosestL=;ClosestR=	77999458	77999458	25,75985010,75986185	0,0,0
chr10	80289274	80289275	chr10	80908600	80908601	DUP	NA	-	+	[Svaba_SR=29,Svaba_PE=36],[Manta_PE=33,Manta_SR=23],[Lumpy_PE=28,Lumpy_SR=15]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=MAT1A;DisruptR=;ClosestL=ZNF519P1;ClosestR=	77999459	82676186	12,80289274,80908602	0,0,0
chr11	4259246	4259247	chr11	4260589	4260590	DEL	NA	+	-	[Manta_PE=5,Manta_SR=32]	manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=SSU72P2;ClosestR=SSU72P2	5558211	5558211	30,4259247,4260586	0,0,0
chr11	5558236	5558237	chr12	28617176	28617177	TRA	NA	-	+	[Svaba_SR=63,Svaba_PE=65],[Manta_PE=59,Manta_SR=58],[Lumpy_PE=37,Lumpy_SR=39]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=OR52B5P,AC104389.4;DisruptR=;ClosestL=OR52H2P;ClosestR=	5558212	28617173	46,5558235,28617181	0,0,0
chr11	9130421	9130422	chr11	10541407	10541408	DEL	NA	+	-	[Svaba_SR=35,Svaba_PE=42],[Manta_PE=35,Manta_SR=33],[Lumpy_PE=21,Lumpy_SR=27]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=SCUBE2;DisruptR=MRVI1-AS1;ClosestL=DENND5A;ClosestR=RNF141	9130420	10460501	27,9130422,10541404	0,0,0
chr11	10460540	10460541	chr16	67552015	67552016	TRA	NA	-	-	[Svaba_SR=32,Svaba_PE=33],[Manta_PE=35,Manta_SR=26],[Lumpy_PE=23,Lumpy_SR=12]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=AMPD3;DisruptR=AC027682.4,AC027682.7;Fusion=AC027682.4-AMPD3|AC027682.7-AMPD3;ClosestL=;ClosestR=RIPOR1	10460501	90226217	23,10460541,67552014	0,0,0
chr11	10542794	10542795	chr16	67606763	67606764	TRA	NA	+	+	[Svaba_SR=38,Svaba_PE=38],[Manta_PE=37,Manta_SR=32],[Lumpy_PE=23,Lumpy_SR=27]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=MRVI1-AS1;DisruptR=CTCF;ClosestL=RNF141;ClosestR=AC009095.1	10460501	90226217	28,10542788,67606765	0,0,0
chr11	16848705	16848706	chr11	16901881	16901882	DUP	NA	-	+	[Svaba_SR=33,Svaba_PE=32],[Manta_PE=31,Manta_SR=23],[Lumpy_PE=27,Lumpy_SR=12]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=PLEKHA7;DisruptR=PLEKHA7;ClosestL=RN7SKP90;ClosestR=	10460501	10460501	0,0,0	0,0,0
chr11	34094976	34094977	chr11	34104287	34104288	DEL	NA	+	-	[Svaba_SR=64,Svaba_PE=70],[Manta_PE=61,Manta_SR=55],[Lumpy_PE=41,Lumpy_SR=38]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=CAPRIN1;DisruptR=;ClosestL=NAT10;ClosestR=NAT10	10460501	10460501	38,34094976,34104286	0,0,0
chr11	55979739	55979740	chr11	55983661	55983662	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=31],[Manta_PE=31,Manta_SR=24],[Lumpy_PE=20,Lumpy_SR=15]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=OR7E5P;DisruptR=;ClosestL=OR10AG1;ClosestR=OR7E5P	78421457	78421457	21,55979740,55983660	0,0,0
chr11	57548726	57548727	chr11	57771620	57771621	DUP	NA	-	+	[Svaba_SR=28,Svaba_PE=28],[Manta_PE=25,Manta_SR=23],[Lumpy_PE=17,Lumpy_SR=16]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=CLP1;DisruptL=SMTNL1;DisruptR=TMX2-CTNND1,AP001931.1,CTNND1;Fusion=TMX2-CTNND1+SMTNL1|AP001931.1+SMTNL1|CTNND1+SMTNL1;ClosestL=UBE2L6;ClosestR=BTBD18	78421457	78421457	19,57548727,57771622	0,0,0
chr11	59727213	59727214	chr11	59784138	59784139	INV	NA	+	+	[Manta_PE=2,Manta_SR=5]	manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=STX3;DisruptR=STX3;ClosestL=OR10Y1P;ClosestR=FABP5P7	78421457	78421457	5,59727215,59784140	0,0,0
chr11	63962462	63962463	chr11	64024132	64024133	DUP	NA	-	+	[Svaba_SR=35,Svaba_PE=35],[Manta_PE=32,Manta_SR=31],[Lumpy_PE=29,Lumpy_SR=23]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=MACROD1;ClosestL=NAA40;ClosestR=AP000721.2	78421457	78421457	26,63962462,64024134	0,0,0
chr11	78000818	78000819	chr11	78055610	78055611	DUP	NA	-	+	[Svaba_SR=71,Svaba_PE=86],[Manta_PE=71,Manta_SR=67],[Lumpy_PE=62,Lumpy_SR=48]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=NDUFC2-KCTD14;ClosestL=INTS4;ClosestR=THRSP	78421457	78421457	51,78000820,78055612	0,0,0
chr11	78421472	78421473	chr11	90936596	90936597	DEL	NA	+	-	[Svaba_SR=71,Svaba_PE=77],[Manta_PE=67,Manta_SR=63],[Lumpy_PE=46,Lumpy_SR=45]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;gap;Cancer_census=EED,PICALM;DisruptL=AP003086.2;DisruptR=;ClosestL=AP003086.1;ClosestR=	78421458	90936583	48,78421473,90936595	0,0,0
chr11	105716409	105716410	chr11	105734303	105734304	DEL	NA	+	-	[Svaba_SR=47,Svaba_PE=56],[Manta_PE=52,Manta_SR=43],[Lumpy_PE=31,Lumpy_SR=34]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=GRIA4;DisruptR=GRIA4;ClosestL=AP000641.1;ClosestR=	90936583	90936583	36,105716410,105734302	0,0,0
chr11	108381260	108381261	chr11	108487235	108487236	DUP	NA	-	+	[Svaba_SR=41,Svaba_PE=76],[Manta_PE=68,Manta_SR=28],[Lumpy_PE=68,Lumpy_SR=21]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=C11orf65;DisruptR=KDELC2;Fusion=C11orf65+KDELC2;ClosestL=ATM;ClosestR=EXPH5	90936583	90936583	23,108381261,108487237	0,0,0
chr11	111916768	111916769	chr11	111978526	111978527	DUP	NA	-	+	[Svaba_SR=35,Svaba_PE=49],[Manta_PE=44,Manta_SR=34],[Lumpy_PE=37,Lumpy_SR=26]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=CRYAB,HSPB2-C11orf52;DisruptR=DIXDC1;Fusion=DIXDC1+HSPB2-C11orf52;ClosestL=C11orf52;ClosestR=	90936583	90936583	28,111916767,111978528	0,0,0
chr11	118925920	118925921	chr11	118940643	118940644	DUP	NA	-	+	[Svaba_SR=25,Svaba_PE=21],[Manta_PE=18,Manta_SR=19],[Lumpy_PE=18,Lumpy_SR=10]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=UPK2;DisruptR=UPK2;ClosestL=BCL9L;ClosestR=RN7SL688P	135076522	135076522	0,0,0	0,0,0
chr11	121159576	121159577	chr11	121161049	121161050	DEL	NA	+	-	[Svaba_SR=72,Svaba_PE=68],[Manta_PE=61,Manta_SR=59],[Lumpy_PE=40,Lumpy_SR=46]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=TECTA;DisruptR=TECTA;ClosestL=;ClosestR=	135076522	135076522	37,121159578,121161048	0,0,0
chr12	11730208	11730209	chr12	11760929	11760930	DUP	NA	-	+	[Manta_PE=92,Manta_SR=101],[Lumpy_PE=83,Lumpy_SR=34]	lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=ETV6;DisruptL=ETV6;DisruptR=ETV6;ClosestL=;ClosestR=	41087	41087	16,11730208,11760932	0,0,0
chr12	19622729	19622730	chr12	19623501	19623502	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=27],[Manta_PE=20,Manta_SR=17],[Lumpy_PE=19,Lumpy_SR=13]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=AEBP2;DisruptR=AEBP2;ClosestL=;ClosestR=	28617172	28617172	14,19622726,19623500	0,0,0
chr12	21883388	21883389	chr12	22000135	22000136	DUP	NA	-	+	[Svaba_SR=2,Svaba_PE=4],[Lumpy_PE=4,Lumpy_SR=2]	svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=AC008250.1,ABCC9;DisruptR=;ClosestL=;ClosestR=AC092862.1	28617172	28617172	2,21883387,22000138	0,0,0
chr12	27487877	27487878	chr12	27551610	27551611	DUP	NA	-	+	[Svaba_SR=35,Svaba_PE=40],[Manta_PE=31,Manta_SR=31],[Lumpy_PE=25,Lumpy_SR=25]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=SMCO2;DisruptR=AC087257.1,PPFIBP1;Fusion=PPFIBP1+SMCO2;ClosestL=RARSP1;ClosestR=	28617172	28617172	22,27487876,27551612	0,0,0
chr12	33688547	33688548	chr12	34143319	34143320	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=26],[Lumpy_PE=3,Lumpy_SR=9]	lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=AC140847.1	28617173	28617173	6,33688546,34143265	0,0,0
chr12	33711445	33711446	chr12	34143764	34143765	INV	NA	+	+	[Svaba_SR=96,Svaba_PE=29],[Manta_PE=28,Manta_SR=0]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=;ClosestL=AC024153.1;ClosestR=AC140847.1	28617173	28617173	0,0,0	0,0,0
chr12	33711446	33711447	chr12	34615081	34615082	INV	NA	+	+	[Svaba_SR=0,Svaba_PE=30],[Manta_PE=30,Manta_SR=65]	manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=;ClosestL=AC024153.1;ClosestR=	28617173	28617173	0,0,0	0,0,0
chr12	33712987	33712988	chr12	34614075	34614076	DEL	NA	+	-	[Svaba_SR=51,Svaba_PE=35],[Manta_PE=18,Manta_SR=42],[Lumpy_PE=15,Lumpy_SR=16]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=;ClosestL=AC024153.1;ClosestR=	28617173	28617173	24,33712989,34614074	0,0,0
chr12	33999946	33999947	chr12	34227764	34227765	INV	NA	-	-	[Svaba_SR=142,Svaba_PE=146],[Manta_PE=139,Manta_SR=120],[Lumpy_PE=104,Lumpy_SR=54]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=;ClosestL=RF00019;ClosestR=AC140847.2	28617173	28617173	66,33999945,34227763	0,0,0
chr12	34143266	34143267	chr12	34614387	34614388	DUP	NA	-	+	[Svaba_SR=64,Svaba_PE=43],[Manta_PE=41,Manta_SR=58]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=;ClosestL=AC140847.1;ClosestR=	28617173	28617173	0,0,0	0,0,0
chr12	34143710	34143711	chr12	34614940	34614941	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=10],[Manta_PE=30,Manta_SR=42],[Lumpy_PE=18,Lumpy_SR=34]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=;ClosestL=AC140847.1;ClosestR=	28617173	28617173	37,34143762,34614940	0,0,0
chr12	34187766	34187767	chr12	34561952	34561953	INV	NA	+	+	[Svaba_SR=114,Svaba_PE=122],[Manta_PE=115,Manta_SR=93],[Lumpy_PE=96,Lumpy_SR=59]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=;ClosestL=AC140847.2;ClosestR=	28617173	28617173	65,34187767,34561954	0,0,0
chr12	34536281	34536282	chr12	34537017	34537018	INV	NA	-	-	[Svaba_SR=69,Svaba_PE=67],[Manta_PE=67,Manta_SR=53],[Lumpy_PE=51,Lumpy_SR=35]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	28617173	28617173	34,34536282,34537016	0,0,0
chr12	34615080	34615081	chr12	34616838	34616839	INV	NA	+	+	[Lumpy_PE=2,Lumpy_SR=19]	lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	28617173	28617173	13,34615077,34616839	0,0,0
chr12	37975722	37975723	chr12	38003307	38003308	DUP	NA	-	+	[Svaba_SR=22,Svaba_PE=29],[Manta_PE=26,Manta_SR=18],[Lumpy_PE=24,Lumpy_SR=13]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	28617173	28617173	16,37975723,38003309	0,0,0
chr12	49218862	49218863	chr12	49287020	49287021	DUP	NA	-	+	[Manta_PE=11,Manta_SR=12]	manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=TUBA1C;DisruptR=;ClosestL=AC010173.1;ClosestR=AC125611.4	28617173	28617173	12,49218881,49287041	0,0,0
chr12	49286891	49286892	chr12	49301181	49301182	DUP	NA	-	+	[Svaba_SR=31,Svaba_PE=20],[Manta_PE=11,Manta_SR=26],[Lumpy_PE=11,Lumpy_SR=17]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=AC125611.4;ClosestL=AC125611.4;ClosestR=PRPH	28617173	28617173	20,49286892,49301183	0,0,0
chr12	113419165	113419166	chr12	113485774	113485775	DUP	NA	-	+	[Svaba_SR=31,Svaba_PE=40],[Manta_PE=38,Manta_SR=30],[Lumpy_PE=35,Lumpy_SR=15]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=SDS;DisruptR=;ClosestL=SDSL;ClosestR=LHX5-AS1	128424612	128424612	24,113419167,113485776	0,0,0
chr12	116013885	116013886	chr12	116039172	116039173	DEL	NA	+	-	[Svaba_SR=40,Svaba_PE=47],[Manta_PE=42,Manta_SR=33],[Lumpy_PE=29,Lumpy_SR=24]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=MED13L;DisruptR=MED13L;ClosestL=;ClosestR=	128424612	128424612	26,116013885,116039171	0,0,0
chr12	119167936	119167937	chr12	119174029	119174030	DUP	NA	-	+	[Svaba_SR=25,Svaba_PE=38],[Manta_PE=35,Manta_SR=20],[Lumpy_PE=33,Lumpy_SR=16]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=SRRM4;ClosestR=AC084880.4	128424612	128424612	19,119167939,119174031	0,0,0
chr12	128424692	128424693	chr12	129071439	129071440	DEL	NA	+	-	[Svaba_SR=33,Svaba_PE=40],[Manta_PE=39,Manta_SR=24],[Lumpy_PE=27,Lumpy_SR=21]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=TMEM132C;DisruptR=;ClosestL=AC090424.1;ClosestR=TMEM132D	128424613	129071366	23,128424693,129071438	0,0,0
chr13	32528399	32528400	chr13	32601724	32601725	DUP	NA	-	+	[Svaba_SR=22,Svaba_PE=30],[Manta_PE=27,Manta_SR=23],[Lumpy_PE=22,Lumpy_SR=14]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=N4BP2L2;DisruptR=PDS5B;ClosestL=N4BP2L2-IT2;ClosestR=	16166247	16166247	19,32528400,32601726	0,0,0
chr13	41538430	41538431	chr13	41559623	41559624	DUP	NA	-	+	[Svaba_SR=22,Svaba_PE=26],[Manta_PE=8,Manta_SR=21]	manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=VWA8	58800227	58800227	20,41538430,41559625	0,0,0
chr13	48375134	48375135	chr13	48378608	48378609	DEL	NA	+	-	[Svaba_SR=29,Svaba_PE=38],[Manta_PE=35,Manta_SR=24],[Lumpy_PE=23,Lumpy_SR=16]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=RB1;DisruptL=RB1;DisruptR=RB1;ClosestL=LPAR6;ClosestR=LPAR6	58800227	58800227	19,48375133,48378607	0,0,0
chr13	76927590	76927591	chr13	76944256	76944257	INV	NA	-	-	[Svaba_SR=0,Svaba_PE=35],[Manta_PE=36,Manta_SR=0]	manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=;ClosestL=BTF3P11;ClosestR=ACOD1	88970765	88970765	0,0,0	0,0,0
chr13	76943976	76943977	chr13	76960662	76960663	INV	NA	+	+	[Svaba_SR=41,Svaba_PE=40],[Manta_PE=41,Manta_SR=39],[Lumpy_PE=38,Lumpy_SR=28]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=;ClosestL=ACOD1;ClosestR=ACOD1	88970765	88970765	29,76943984,76960664	0,0,0
chr13	102428501	102428502	chr13	102801823	102801824	DUP	NA	-	+	[Svaba_SR=48,Svaba_PE=87],[Manta_PE=78,Manta_SR=45],[Lumpy_PE=72,Lumpy_SR=36]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=BIVM,BIVM-ERCC5;ClosestL=;ClosestR=KDELC1	102428502	102801718	37,102428503,102801825	0,0,0
chr14	32214734	32214735	chr14	32219731	32219732	DEL	NA	+	-	[Svaba_SR=61,Svaba_PE=86],[Manta_PE=74,Manta_SR=69],[Lumpy_PE=69,Lumpy_SR=8]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=RNU6-8;ClosestR=RNU6-8	39133588	39133588	39,32214734,32219730	0,0,0
chr14	34442880	34442881	chr14	34535891	34535892	DUP	NA	-	+	[Svaba_SR=15,Svaba_PE=22],[Manta_PE=19,Manta_SR=11],[Lumpy_PE=16,Lumpy_SR=7]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=SPTSSA,EGLN3;DisruptR=EAPP;Fusion=SPTSSA+EAPP|EGLN3+EAPP;ClosestL=;ClosestR=AL445363.3	39133588	39133588	10,34442882,34535893	0,0,0
chr14	39133636	39133637	chr14	39342797	39342798	DUP	NA	-	+	[Svaba_SR=73,Svaba_PE=87],[Manta_PE=72,Manta_SR=66],[Lumpy_PE=59,Lumpy_SR=40]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=GEMIN2;DisruptR=MIA2;Fusion=MIA2+GEMIN2;ClosestL=TRAPPC6B;ClosestR=	39133589	39342723	39,39133635,39342806	0,0,0
chr14	49931594	49931595	chr14	50028318	50028319	DUP	NA	-	+	[Svaba_SR=35,Svaba_PE=47],[Manta_PE=41,Manta_SR=31],[Lumpy_PE=29,Lumpy_SR=27]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=LINC01588;DisruptR=LINC01588;ClosestL=RF00017;ClosestR=	41200381	41200381	25,49931595,50028323	0,0,0
chr14	64117734	64117735	chr14	64374357	64374358	DUP	NA	-	+	[Svaba_SR=60,Svaba_PE=72],[Manta_PE=63,Manta_SR=54],[Lumpy_PE=51,Lumpy_SR=45]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=ESR2,SYNE2;DisruptR=TEX21P;Fusion=ESR2+TEX21P;ClosestL=;ClosestR=AL161756.2	64117655	64374366	41,64117735,64374359	0,0,0
chr14	68302189	68302190	chr14	68621145	68621146	DUP	NA	-	+	[Svaba_SR=71,Svaba_PE=99],[Manta_PE=89,Manta_SR=67],[Lumpy_PE=81,Lumpy_SR=43]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=RAD51B;DisruptL=RAD51B;DisruptR=RAD51B;ClosestL=;ClosestR=AL121820.2	68301568	68621030	38,68302189,68621152	0,0,0
chr14	73199754	73199755	chr20	6218580	6218581	TRA	NA	-	+	[Svaba_SR=38,Svaba_PE=42],[Manta_PE=34,Manta_SR=39],[Lumpy_PE=22,Lumpy_SR=27]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=PSEN1;DisruptR=;ClosestL=AC004858.1;ClosestR=AL109618.2	73199737	6218513	33,73199753,6218582	0,0,0
chr14	73706446	73706447	chr14	73726852	73726853	INV	NA	+	+	[Svaba_SR=120,Svaba_PE=129],[Manta_PE=78,Manta_SR=103],[Lumpy_PE=67,Lumpy_SR=54]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=ELMSAN1;ClosestL=DNAL1;ClosestR=PNMA1	73199737	73199737	63,73706448,73726855	0,0,0
chr14	73708979	73708980	chr14	73726875	73726876	INV	NA	-	-	[Svaba_SR=112,Svaba_PE=86],[Manta_PE=87,Manta_SR=101],[Lumpy_PE=60,Lumpy_SR=22]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=ELMSAN1;ClosestL=PNMA1;ClosestR=PNMA1	73199737	73199737	2,73708977,73726877	0,0,0
chr14	80321677	80321678	chr14	80331498	80331499	DEL	NA	+	-	[Svaba_SR=103,Svaba_PE=94],[Manta_PE=81,Manta_SR=83],[Lumpy_PE=59,Lumpy_SR=60]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=DIO2,DIO2-AS1;DisruptR=DIO2,DIO2-AS1;ClosestL=;ClosestR=	73199737	73199737	57,80321676,80331497	0,0,0
chr14	99315057	99315058	chr14	99319824	99319825	DEL	NA	+	-	[Svaba_SR=90,Svaba_PE=151],[Manta_PE=149,Manta_SR=73],[Lumpy_PE=120,Lumpy_SR=45]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;ClosestL=AL132819.1;ClosestR=AL132819.1	106883618	106883618	54,99315059,99319819	0,0,0
chr14	99534775	99534776	chr14	99658345	99658346	DUP	NA	-	+	[Svaba_SR=45,Svaba_PE=43],[Manta_PE=35,Manta_SR=41],[Lumpy_PE=27,Lumpy_SR=35]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=CCDC85C,CCNK;DisruptR=HHIPL1;Fusion=HHIPL1+CCNK;ClosestL=;ClosestR=	106883618	106883618	34,99534777,99658347	0,0,0
chr14	103542159	103542160	chr14	103543091	103543092	DUP	NA	-	+	[Svaba_SR=105,Svaba_PE=148],[Manta_PE=139,Manta_SR=85],[Lumpy_PE=126,Lumpy_SR=68]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=TRMT61A;ClosestR=TRMT61A	106883618	106883618	51,103542159,103543093	0,0,0
chr15	49998583	49998584	chr15	50057998	50057999	DUP	NA	-	+	[Svaba_SR=38,Svaba_PE=18],[Manta_PE=14,Manta_SR=24]	manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=ATP8B4;DisruptR=ATP8B4;ClosestL=RNA5SP394;ClosestR=	34526120	34526120	26,49998583,50058000	0,0,0
chr15	71887826	71887827	chr15	72152284	72152285	DEL	NA	+	-	[Svaba_SR=65,Svaba_PE=85],[Manta_PE=77,Manta_SR=56],[Lumpy_PE=54,Lumpy_SR=46]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=MYO9A;DisruptR=AC020779.2;Fusion=AC020779.2+MYO9A;ClosestL=;ClosestR=GRAMD2A	71887858	72152244	44,71887824,72152283	0,0,0
chr15	84936470	84936471	chr15	85490843	85490844	DUP	NA	-	+	[Svaba_SR=41,Svaba_PE=41],[Manta_PE=34,Manta_SR=35],[Lumpy_PE=27,Lumpy_SR=25]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=SLC28A1;DisruptR=AKAP13;Fusion=AKAP13+SLC28A1;ClosestL=RNU6-339P;ClosestR=	84936397	85513789	29,84936466,85490845	0,0,0
chr15	90138924	90138925	chr15	90290343	90290344	DUP	NA	-	+	[Svaba_SR=107,Svaba_PE=106],[Manta_PE=87,Manta_SR=95],[Lumpy_PE=72,Lumpy_SR=50]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=AC091167.6;ClosestL=IDH2-DT;ClosestR=GOLGA2P8	90138916	90290295	64,90138923,90290345	0,0,0
chr15	91576954	91576955	chr15	91579869	91579870	DEL	NA	+	-	[Svaba_SR=65,Svaba_PE=70],[Manta_PE=47,Manta_SR=51],[Lumpy_PE=38,Lumpy_SR=10]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=AC104035.1;DisruptR=AC104035.1;ClosestL=;ClosestR=	90290295	90290295	39,91576953,91579868	0,0,0
chr16	12897046	12897047	chr16	30066679	30066680	DUP	NA	-	+	[Svaba_SR=18,Svaba_PE=43],[Manta_PE=38,Manta_SR=15],[Lumpy_PE=39,Lumpy_SR=8]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;gap;Cancer_census=ERCC4,PALB2,IL21R,MYH11,PRKCB;DisruptL=;DisruptR=AC093512.2,ALDOA;ClosestL=SHISA9;ClosestR=AC093512.1	12896987	30066716	12,12897046,30066681	0,0,0
chr16	67103909	67103910	chr16	67237337	67237338	DUP	NA	-	+	[Svaba_SR=45,Svaba_PE=42],[Manta_PE=42,Manta_SR=38],[Lumpy_PE=41,Lumpy_SR=9]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=FHOD1;ClosestL=CBFB;ClosestR=SLC9A5	90226217	90226217	37,67103913,67237339	0,0,0
chr16	81023880	81023881	chr16	81088348	81088349	DUP	NA	-	+	[Svaba_SR=28,Svaba_PE=28],[Manta_PE=26,Manta_SR=24],[Lumpy_PE=18,Lumpy_SR=20]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=CENPN,AC092718.2,AC092718.8;DisruptR=AC092718.8,AC092718.3,GCSH;Fusion=AC092718.2+AC092718.8|AC092718.2+AC092718.3|AC092718.2+GCSH|AC092718.8+AC092718.3|AC092718.8+GCSH;ClosestL=CMC2;ClosestR=AC092718.1	90226217	90226217	24,81023880,81088350	0,0,0
chr17	20712372	20712373	chr17	20720249	20720250	DUP	NA	-	+	[Svaba_SR=28,Svaba_PE=27],[Manta_PE=25,Manta_SR=29]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=AC087499.2;ClosestL=AC087499.6;ClosestR=AC087499.6	39261864	39261864	20,20712384,20720251	0,0,0
chr17	39261884	39261885	chr17	39350108	39350109	DEL	NA	+	-	[Svaba_SR=79,Svaba_PE=74],[Manta_PE=62,Manta_SR=69],[Lumpy_PE=38,Lumpy_SR=42]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=FBXL20;DisruptR=FBXL20;ClosestL=AC015910.1;ClosestR=	39261865	39349815	50,39261886,39350106	0,0,0
chr17	50701666	50701667	chr17	50762091	50762092	DUP	NA	-	+	[Svaba_SR=72,Svaba_PE=78],[Manta_PE=67,Manta_SR=64],[Lumpy_PE=55,Lumpy_SR=49]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=ANKRD40;DisruptR=LINC00483;Fusion=ANKRD40+LINC00483;ClosestL=RF00019;ClosestR=LUC7L3	39349815	39349815	48,50701670,50762093	0,0,0
chr17	77358115	77358116	chr17	77398291	77398292	DUP	NA	-	+	[Svaba_SR=34,Svaba_PE=42],[Manta_PE=35,Manta_SR=28],[Lumpy_PE=33,Lumpy_SR=24]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SEPT9;DisruptL=SEPT9;DisruptR=SEPT9;ClosestL=AC111182.1;ClosestR=MIR4316	83247341	83247341	24,77358115,77398293	0,0,0
chr17	81497957	81497958	chr17	81583672	81583673	DUP	NA	-	+	[Svaba_SR=16,Svaba_PE=34],[Manta_PE=32,Manta_SR=22],[Lumpy_PE=30,Lumpy_SR=9]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=NPLOC4;ClosestL=ACTG1;ClosestR=RF00019	83247341	83247341	2,81497944,81583674	0,0,0
chr18	616133	616134	chr18	641824	641825	DUP	NA	-	+	[Svaba_SR=25,Svaba_PE=31],[Manta_PE=30,Manta_SR=17],[Lumpy_PE=24,Lumpy_SR=15]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=CLUL1;DisruptR=CLUL1,TYMSOS;ClosestL=;ClosestR=AP001178.3	10010	10010	18,616135,641826	0,0,0
chr18	8939082	8939083	chr18	10814209	10814210	DUP	NA	-	+	[Svaba_SR=33,Svaba_PE=35],[Manta_PE=27,Manta_SR=27],[Lumpy_PE=21,Lumpy_SR=2]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=PIEZO2;ClosestL=;ClosestR=	8939026	10814016	24,8939084,10814211	0,0,0
chr18	9778010	9778011	chr18	9783361	9783362	INV	NA	+	+	[Svaba_SR=27,Svaba_PE=23],[Manta_PE=25,Manta_SR=23],[Lumpy_PE=27,Lumpy_SR=15]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=RAB31;DisruptR=RAB31;ClosestL=ZNF415P1;ClosestR=ZNF415P1	8939026	8939026	20,9778010,9783363	0,0,0
chr18	9783139	9783140	chr18	9788175	9788176	INV	NA	-	-	[Svaba_SR=29,Svaba_PE=22],[Manta_PE=17,Manta_SR=24],[Lumpy_PE=13,Lumpy_SR=14]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=RAB31;DisruptR=RAB31;ClosestL=ZNF415P1;ClosestR=ZNF415P1	8939026	8939026	21,9783138,9788174	0,0,0
chr18	35873694	35873695	chr18	35962466	35962467	DUP	NA	-	+	[Svaba_SR=53,Svaba_PE=65],[Manta_PE=63,Manta_SR=45],[Lumpy_PE=52,Lumpy_SR=32]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=AC118757.1;ClosestL=;ClosestR=C18orf21	55686228	55686228	37,35873694,35962468	0,0,0
chr18	55686264	55686265	chr18	55692541	55692542	INV	NA	+	+	[Svaba_SR=29,Svaba_PE=23],[Manta_PE=23,Manta_SR=28],[Lumpy_PE=21,Lumpy_SR=13]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;ClosestL=;ClosestR=	55686229	55686229	18,55686278,55692543	0,0,0
chr18	60608573	60608574	chrX	11935070	11935071	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=19],[Manta_PE=14,Manta_SR=0]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=AC010928.1;ClosestR=	55686229	10446	2,60608575,11935071	0,0,0
chr19	10426988	10426989	chr19	10538521	10538522	DUP	NA	-	+	[Svaba_SR=28,Svaba_PE=38],[Manta_PE=34,Manta_SR=21],[Lumpy_PE=27,Lumpy_SR=17]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=KEAP1;DisruptL=PDE4A;DisruptR=;ClosestL=CDC37;ClosestR=ATG4D	5824139	5824139	18,10426987,10538523	0,0,0
chr19	16856241	16856242	chr19	16968701	16968702	DUP	NA	-	+	[Svaba_SR=69,Svaba_PE=36],[Manta_PE=75,Manta_SR=60],[Lumpy_PE=63,Lumpy_SR=34]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=SIN3B;DisruptR=CPAMD8;ClosestL=AC008737.1;ClosestR=	5824139	5824139	2,16856239,16968702	0,0,0
chr19	18743352	18743353	chr19	18809683	18809684	DUP	NA	-	+	[Svaba_SR=34,Svaba_PE=25],[Manta_PE=25,Manta_SR=28],[Lumpy_PE=17,Lumpy_SR=17]	svaba,lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=CRTC1;DisruptL=CRTC1;DisruptR=;ClosestL=;ClosestR=COMP	5824139	5824139	23,18743353,18809685	0,0,0
chr19	58076219	58076220	chr19	58209952	58209953	DUP	NA	-	+	[Svaba_SR=29,Svaba_PE=45],[Manta_PE=40,Manta_SR=25],[Lumpy_PE=34,Lumpy_SR=20]	svaba,manta,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=ZNF135;DisruptR=ZNF274;Fusion=ZNF274+ZNF135;ClosestL=RN7SL526P;ClosestR=RPS15AP36	58607515	58607515	22,58076223,58209954	0,0,0
chr20	9153165	9153166	chr20	9202353	9202354	DEL	NA	+	-	[Svaba_SR=66,Svaba_PE=78],[Manta_PE=75,Manta_SR=57],[Lumpy_PE=56,Lumpy_SR=21]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=PLCB4;DisruptR=PLCB4;ClosestL=;ClosestR=	6218513	6218513	46,9153165,9202352	0,0,0
chr20	9843321	9843322	chr20	9852610	9852611	INV	NA	+	+	[Svaba_SR=29,Svaba_PE=21],[Manta_PE=28,Manta_SR=27],[Lumpy_PE=26,Lumpy_SR=22]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;ClosestL=PAK5;ClosestR=PAK5	6218513	6218513	23,9843321,9852612	0,0,0
chr20	19183298	19183299	chr20	19282322	19282323	DUP	NA	-	+	[Svaba_SR=33,Svaba_PE=26],[Manta_PE=17,Manta_SR=35],[Lumpy_PE=15,Lumpy_SR=17]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=SLC24A3,AL049647.1;ClosestL=;ClosestR=	6218513	6218513	0,0,0	0,0,0
chr20	32141963	32141964	chr20	32229874	32229875	DUP	NA	-	+	[Svaba_SR=31,Svaba_PE=44],[Manta_PE=36,Manta_SR=28],[Lumpy_PE=33,Lumpy_SR=23]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=TM9SF4;DisruptR=POFUT1;Fusion=POFUT1+TM9SF4;ClosestL=;ClosestR=MIR1825	32713333	32713333	28,32141965,32229876	0,0,0
chr20	32340799	32340800	chr20	32595112	32595113	DUP	NA	-	+	[Svaba_SR=30,Svaba_PE=40],[Manta_PE=41,Manta_SR=20],[Lumpy_PE=38,Lumpy_SR=13]	manta,lumpy,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=ASXL1;DisruptL=;DisruptR=NOL4L-DT;ClosestL=KIF3B;ClosestR=AL133343.1	32713333	32713333	17,32340799,32595114	0,0,0
chr20	54223947	54223948	chr20	54231711	54231712	DEL	NA	+	-	[Svaba_SR=72,Svaba_PE=90],[Manta_PE=77,Manta_SR=64],[Lumpy_PE=52,Lumpy_SR=58]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=PFDN4;DisruptR=;ClosestL=;ClosestR=PFDN4	64334067	64334067	43,54223948,54231710	0,0,0
chr20	54837554	54837555	chr20	54869346	54869347	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=28],[Manta_PE=26,Manta_SR=18],[Lumpy_PE=21,Lumpy_SR=11]	manta,svaba,lumpy	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=;ClosestL=;ClosestR=RNU4ATAC7P	64334067	64334067	17,54837555,54869345	0,0,0
chr21	18895977	18895978	chr21	18897092	18897093	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=36],[Manta_PE=22,Manta_SR=15],[Lumpy_PE=29,Lumpy_SR=6]	lumpy,svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;ClosestL=;ClosestR=	13044018	13044018	7,18895977,18897091	0,0,0
chr21	35647327	35647328	chr21	35770578	35770579	DUP	NA	-	+	[Svaba_SR=33,Svaba_PE=38],[Manta_PE=33,Manta_SR=31],[Lumpy_PE=28,Lumpy_SR=25]	lumpy,manta,svaba	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=RUNX1;DisruptR=RUNX1;ClosestL=;ClosestR=	46699872	46699872	24,35647329,35770580	0,0,0
chr22	36439278	36439279	chr22	36531210	36531211	DUP	NA	-	+	[Svaba_SR=35,Svaba_PE=34],[Manta_PE=27,Manta_SR=29]	svaba,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=;ClosestL=RF00019;ClosestR=EIF3D	50807810	50807810	24,36439278,36531212	0,0,0
chr22	50279654	50279655	chr22	50280218	50280219	DEL	NA	+	-	[Manta_PE=65,Manta_SR=79],[Lumpy_PE=44,Lumpy_SR=67]	lumpy,manta	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=PLXNB2;DisruptR=PLXNB2;ClosestL=MAPK11;ClosestR=MAPK11	50807810	50807810	54,50279656,50280218	0,0,0