#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	44887191	44887192	chrX	47658825	47658826	DUP	NA	-	+	[Svaba_SR=29,Svaba_PE=25],[Manta_PE=20,Manta_SR=25],[Lumpy_PE=14,Lumpy_SR=21]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=ARAF|Tier2,KDM6A|Tier1,RBM10|Tier1;DisruptL=KDM6A;DisruptR=UXT;ClosestL=;ClosestR=UXT-AS1	44887175	47658809	20,44887191,47658826	0,0,0
chrX	45136456	45136457	chrX	45137951	45137952	DEL	NA	+	-	[Svaba_SR=35,Svaba_PE=44],[Manta_PE=45,Manta_SR=27],[Lumpy_PE=35,Lumpy_SR=14]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=CXorf36;ClosestR=CXorf36	44887175	44887175	15,45136456,45137951	0,0,0
chrX	57361939	57361940	chrX	57364610	57364611	INV	NA	-	-	[Svaba_SR=12,Svaba_PE=29],[Manta_PE=29,Manta_SR=10],[Lumpy_PE=24,Lumpy_SR=7]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=FAAH2;DisruptR=FAAH2;ClosestL=;ClosestR=	57361937	57361937	9,57361930,57364610	0,0,0
chrX	76242860	76242861	chrX	116501145	116501146	DUP	NA	-	+	[Svaba_SR=27,Svaba_PE=22],[Manta_PE=16,Manta_SR=26],[Lumpy_PE=15,Lumpy_SR=12]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=IRS4|Tier1,BTK|Tier1,ATRX|Tier1;DisruptL=;DisruptR=;ClosestL=RNU6-867P;ClosestR=	76245723	116456071	14,76242855,116501149	0,0,0
chrX	76244485	76244486	chrX	116500843	116500844	INV	NA	-	-	[Svaba_SR=24,Svaba_PE=22],[Manta_PE=25,Manta_SR=18],[Lumpy_PE=16,Lumpy_SR=11]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=IRS4|Tier1,BTK|Tier1,ATRX|Tier1;DisruptL=;DisruptR=;ClosestL=RNU6-867P;ClosestR=	76245723	116456071	17,76244484,116500843	0,0,0
chrX	79973209	79973210	chrX	79982346	79982347	DEL	NA	+	-	[Svaba_SR=18,Svaba_PE=23],[Manta_PE=22,Manta_SR=17],[Lumpy_PE=13,Lumpy_SR=5]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	76245724	76245724	0,0,0	0,0,0
chrX	80459951	80459952	chrX	80462152	80462153	DEL	NA	+	-	[Svaba_SR=8,Svaba_PE=92],[Manta_PE=75,Manta_SR=69],[Lumpy_PE=45,Lumpy_SR=60]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=TENT5D;ClosestR=TENT5D	84380545	84380545	45,80459950,80462152	0,0,0
chrX	84276246	84276247	chrX	84287224	84287225	INV	NA	-	-	[Svaba_SR=22,Svaba_PE=13],[Manta_PE=9,Manta_SR=21]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	84380545	84380545	0,0,0	0,0,0
chrX	84380522	84380523	chrX	84382004	84382005	INV	NA	+	+	[Svaba_SR=0,Svaba_PE=9],[Manta_PE=20,Manta_SR=26],[Lumpy_PE=17,Lumpy_SR=15]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=HDX;DisruptR=HDX;ClosestL=;ClosestR=	84380545	84380546	19,84380640,84382006	0,0,0
chrX	89287531	89287532	chrX	89298078	89298079	DUP	NA	-	+	[Svaba_SR=28,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	88321166	88321166	23,89287531,89298079	0,0,0
chrX	91727150	91727151	chrX	91796419	91796420	DUP	NA	-	+	[Svaba_SR=20,Svaba_PE=21],[Manta_PE=15,Manta_SR=19],[Lumpy_PE=14,Lumpy_SR=9]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=PCDH11X;ClosestL=;ClosestR=RNU2-26P	88321166	88321166	17,91727141,91796420	0,0,0
chrX	100877602	100877603	chrX	153586485	153586486	INV	NA	+	+	[Svaba_SR=38,Svaba_PE=50],[Manta_PE=47,Manta_SR=37],[Lumpy_PE=40,Lumpy_SR=29]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=IRS4|Tier1,DCAF12L2|Tier2,BTK|Tier1,STAG2|Tier1,ELF4|Tier1,PHF6|Tier1,ATP2B3|Tier1,SEPT6|Tier2,GPC3|Tier1,BCORL1|Tier1;DisruptL=;DisruptR=;ClosestL=NOX1;ClosestR=CCNQ	100877556	153586441	31,100877602,153586486	0,0,0
chrX	117971506	117971507	chrX	118882097	118882098	DUP	NA	-	+	[Svaba_SR=71,Svaba_PE=70],[Manta_PE=58,Manta_SR=71],[Lumpy_PE=52,Lumpy_SR=47]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=KLHL13;DisruptR=LINC01285;ClosestL=;ClosestR=AC006965.1	117971510	118882103	49,117971503,118882107	0,0,0
chrX	139747038	139747039	chrX	153271819	153271820	INV	NA	+	+	[Manta_PE=10,Manta_SR=37]	manta	HCC-1143_80--HCC-1143BL_40	known=;gap;DisruptL=ATP11C;DisruptR=;ClosestL=;ClosestR=AC236972.4	139747068	153149106	31,139747040,153271820	0,0,0
chr1	6465318	6465319	chr3	85183520	85183521	TRA	NA	+	-	[Svaba_SR=77,Svaba_PE=25],[Manta_PE=24,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TNFRSF25;DisruptR=CADM2;ClosestL=PLEKHG5;ClosestR=	6465257	85183423	0,0,0	0,0,0
chr1	6465318	6465319	chr3	85187355	85187356	TRA	NA	+	+	[Svaba_SR=43,Svaba_PE=0],[Manta_PE=26,Manta_SR=35],[Lumpy_PE=11,Lumpy_SR=24]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TNFRSF25;DisruptR=CADM2;Fusion=CADM2-TNFRSF25;ClosestL=PLEKHG5;ClosestR=	6465257	85183423	26,6465320,85187356	0,0,0
chr1	6509231	6509232	chr1	6510626	6510627	INV	NA	-	-	[Manta_PE=16,Manta_SR=18],[Lumpy_PE=12,Lumpy_SR=12]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PLEKHG5;DisruptR=PLEKHG5;ClosestL=NOL9;ClosestR=NOL9	6465257	6465257	10,6509237,6510621	0,0,0
chr1	6509232	6509233	chr21	34847762	34847763	TRA	NA	-	-	[Manta_PE=18,Manta_SR=18]	manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=RUNX1|Tier1;DisruptL=PLEKHG5;DisruptR=RUNX1;ClosestL=NOL9;ClosestR=	6465257	34847755	0,0,0	0,0,0
chr1	6510727	6510728	chr21	34847762	34847763	TRA	NA	+	-	[Svaba_SR=26,Svaba_PE=10],[Manta_PE=2,Manta_SR=22]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=RUNX1|Tier1;DisruptL=PLEKHG5;DisruptR=RUNX1;Fusion=RUNX1-PLEKHG5;ClosestL=NOL9;ClosestR=	6465257	34847755	13,6510727,34847762	0,0,0
chr1	6623384	6623385	chr1	227866329	227866330	INV	NA	-	-	[Manta_PE=11,Manta_SR=31],[Lumpy_PE=3,Lumpy_SR=27]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=ID3|Tier2,MDS2|Tier2,MYCL|Tier1,TAL1|Tier1,JUN|Tier1,BCL10|Tier1,RPL5|Tier1,RBM15|Tier1,NRAS|Tier1,FAM46C|Tier1,MLLT11|Tier1,S100A7|Tier2,SLC45A3|Tier1,CASP9|Tier2,PAX7|Tier1,LCK|Tier1,SFPQ|Tier1,THRAP3|Tier2,CSF3R|Tier1,MPL|Tier1,MUTYH|Tier1,STIL|Tier1,CDKN2C|Tier1,FUBP1|Tier1,BCL9|Tier1,TPM3|Tier1,LMNA|Tier1,PRCC|Tier1,NTRK1|Tier1,FCRL4|Tier1,FCGR2B|Tier1,DDR2|Tier1,PRRX1|Tier1,ABL2|Tier1,TPR|Tier1,ELF3|Tier2,MDM4|Tier1,ELK4|Tier1,H3F3A|Tier1,MTOR|Tier1,PRDM2|Tier2,SPEN|Tier1,SDHB|Tier1,ARHGEF10L|Tier2,ARID1A|Tier1,JAK1|Tier1,TRIM33|Tier1,NOTCH2|Tier1,ARNT|Tier1,SDHC|Tier1,CDC73|Tier1,PTPRC|Tier1,CAMTA1|Tier1,EPS15|Tier1,ATP1A1|Tier1,PDE4DIP|Tier1,MUC1|Tier1,PBX1|Tier1;DisruptL=PHF13;DisruptR=;ClosestL=THAP3;ClosestR=PRSS38	6465257	223431463	18,6623385,227866329	0,0,0
chr1	6623385	6623386	chr1	227866441	227866442	INV	NA	+	+	[Manta_PE=14,Manta_SR=27],[Lumpy_PE=3,Lumpy_SR=20]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=ID3|Tier2,MDS2|Tier2,MYCL|Tier1,TAL1|Tier1,JUN|Tier1,BCL10|Tier1,RPL5|Tier1,RBM15|Tier1,NRAS|Tier1,FAM46C|Tier1,MLLT11|Tier1,S100A7|Tier2,SLC45A3|Tier1,CASP9|Tier2,PAX7|Tier1,LCK|Tier1,SFPQ|Tier1,THRAP3|Tier2,CSF3R|Tier1,MPL|Tier1,MUTYH|Tier1,STIL|Tier1,CDKN2C|Tier1,FUBP1|Tier1,BCL9|Tier1,TPM3|Tier1,LMNA|Tier1,PRCC|Tier1,NTRK1|Tier1,FCRL4|Tier1,FCGR2B|Tier1,DDR2|Tier1,PRRX1|Tier1,ABL2|Tier1,TPR|Tier1,ELF3|Tier2,MDM4|Tier1,ELK4|Tier1,H3F3A|Tier1,MTOR|Tier1,PRDM2|Tier2,SPEN|Tier1,SDHB|Tier1,ARHGEF10L|Tier2,ARID1A|Tier1,JAK1|Tier1,TRIM33|Tier1,NOTCH2|Tier1,ARNT|Tier1,SDHC|Tier1,CDC73|Tier1,PTPRC|Tier1,CAMTA1|Tier1,EPS15|Tier1,ATP1A1|Tier1,PDE4DIP|Tier1,MUC1|Tier1,PBX1|Tier1;DisruptL=PHF13;DisruptR=;ClosestL=THAP3;ClosestR=PRSS38	6465257	223431463	19,6623387,227866442	0,0,0
chr1	8115745	8115746	chr1	8337706	8337707	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=11],[Manta_PE=8,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AL034417.2;DisruptR=SLC45A1;Fusion=SLC45A1+AL034417.2;ClosestL=;ClosestR=RF00019	8673995	8673995	6,8115746,8337582	0,0,0
chr1	8115746	8115747	chr1	8341045	8341046	INV	NA	-	-	[Svaba_SR=28,Svaba_PE=19],[Manta_PE=20,Manta_SR=16],[Lumpy_PE=15,Lumpy_SR=11]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AL034417.2;DisruptR=SLC45A1;ClosestL=;ClosestR=RERE	8673995	8673995	13,8115746,8341045	0,0,0
chr1	8337686	8337687	chr1	8341281	8341282	INV	NA	+	+	[Manta_PE=17,Manta_SR=21]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SLC45A1;DisruptR=SLC45A1;ClosestL=RF00019;ClosestR=RERE	8673995	8673995	11,8337688,8341282	0,0,0
chr1	8673961	8673962	chr1	8950735	8950736	DUP	NA	-	+	[Svaba_SR=48,Svaba_PE=55],[Manta_PE=45,Manta_SR=43],[Lumpy_PE=38,Lumpy_SR=35]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RERE;DisruptR=CA6;ClosestL=;ClosestR=	8673995	8950766	28,8673963,8950736	0,0,0
chr1	19771904	19771905	chr1	23063404	23063405	DUP	NA	-	+	[Svaba_SR=20,Svaba_PE=16],[Manta_PE=17,Manta_SR=17],[Lumpy_PE=11,Lumpy_SR=8]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TMCO4;DisruptR=KDM1A,AL031428.1;Fusion=TMCO4+AL031428.1;ClosestL=;ClosestR=MIR4419A	19769881	23063291	14,19771904,23063409	0,0,0
chr1	40528747	40528748	chr16	187562	187563	TRA	NA	-	-	[Svaba_SR=21,Svaba_PE=11],[Manta_PE=10,Manta_SR=18],[Lumpy_PE=8,Lumpy_SR=16]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=ZNF684;ClosestR=Z69706.1	47818851	10005	17,40528747,187560	0,0,0
chr1	40529024	40529025	chrY	56870831	56870832	TRA	NA	+	-	[Svaba_SR=18,Svaba_PE=16]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=ZNF684;ClosestR=CTBP2P1	47818851	-1	16,40529026,56870831	0,0,0
chr1	47818840	47818841	chr1	70293544	70293545	DUP	NA	-	+	[Svaba_SR=22,Svaba_PE=19],[Manta_PE=18,Manta_SR=15],[Lumpy_PE=15,Lumpy_SR=12]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=JUN|Tier1,CDKN2C|Tier1,JAK1|Tier1,EPS15|Tier1;DisruptL=AC096541.1,TRABD2B;DisruptR=ANKRD13C;Fusion=TRABD2B+ANKRD13C;ClosestL=;ClosestR=	47818851	83866422	12,47818841,70293545	0,0,0
chr1	51383095	51383096	chr1	70292967	70292968	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=21],[Manta_PE=22,Manta_SR=16],[Lumpy_PE=19,Lumpy_SR=5]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=JUN|Tier1,JAK1|Tier1,EPS15|Tier1;DisruptL=EPS15;DisruptR=ANKRD13C;Fusion=ANKRD13C+EPS15;ClosestL=RNU6-877P;ClosestR=	51383049	83866422	0,0,0	0,0,0
chr1	52860644	52860645	chr1	53006333	53006334	DEL	NA	+	-	[Svaba_SR=16,Svaba_PE=16],[Manta_PE=16,Manta_SR=13],[Lumpy_PE=13,Lumpy_SR=4]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ZYG11A;DisruptR=SCP2;Fusion=ZYG11A+SCP2;ClosestL=;ClosestR=TUBBP10	51383049	51383049	11,52860642,53006333	0,0,0
chr1	54258679	54258680	chr1	54270175	54270176	DEL	NA	+	-	[Manta_PE=7,Manta_SR=3],[Lumpy_PE=6,Lumpy_SR=2]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SSBP3;DisruptR=SSBP3;ClosestL=SSBP3-AS1;ClosestR=AL161644.1	51383049	51383049	2,54258681,54270176	0,0,0
chr1	58133514	58133515	chr1	58140197	58140198	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=28],[Manta_PE=27,Manta_SR=20],[Lumpy_PE=17,Lumpy_SR=15]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=DAB1;DisruptR=DAB1;ClosestL=;ClosestR=	51383049	51383049	18,58133514,58140197	0,0,0
chr1	68760869	68760870	chr6	158632522	158632523	TRA	NA	-	-	[Manta_PE=12,Manta_SR=20],[Lumpy_PE=4,Lumpy_SR=1]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AL033530.1;DisruptR=TMEM181;ClosestL=;ClosestR=DYNLT1	83866422	166891771	0,0,0	0,0,0
chr1	68761024	68761025	chr6	158632501	158632502	TRA	NA	+	+	[Svaba_SR=22,Svaba_PE=9],[Manta_PE=10,Manta_SR=17],[Lumpy_PE=7,Lumpy_SR=15]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AL033530.1;DisruptR=TMEM181;ClosestL=;ClosestR=DYNLT1	83866422	166891771	16,68761023,158632502	0,0,0
chr1	83866390	83866391	chr1	84289947	84289948	DUP	NA	-	+	[Svaba_SR=40,Svaba_PE=43],[Manta_PE=40,Manta_SR=36],[Lumpy_PE=35,Lumpy_SR=26]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TTLL7;DisruptR=;ClosestL=LINC01725;ClosestR=SAMD13	83866422	84289902	30,83866393,84289948	0,0,0
chr1	94125559	94125560	chr1	94476963	94476964	DUP	NA	-	+	[Svaba_SR=41,Svaba_PE=52],[Manta_PE=44,Manta_SR=38],[Lumpy_PE=39,Lumpy_SR=23]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=ABCD3;ClosestL=ABCA4;ClosestR=	94125587	94476856	32,94125555,94476964	0,0,0
chr1	94708322	94708323	chr15	83903969	83903970	TRA	NA	+	-	[Svaba_SR=13,Svaba_PE=2]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SLC44A3-AS1;DisruptR=ADAMTSL3;ClosestL=;ClosestR=	94476856	72362590	3,94708272,83903969	0,0,0
chr1	101718078	101718079	chr20	29887491	29887492	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=25],[Manta_PE=24,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=3]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC01709;DisruptR=;ClosestL=RNU6-965P;ClosestR=DUX4L37	103478104	29339193	6,101718079,29887492	0,0,0
chr1	101718262	101718263	chr1	107356428	107356429	DEL	NA	+	-	[Svaba_SR=12,Svaba_PE=19],[Manta_PE=18,Manta_SR=11],[Lumpy_PE=15,Lumpy_SR=4]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC01709;DisruptR=NTNG1;Fusion=LINC01709+NTNG1;ClosestL=RNU6-965P;ClosestR=	103478104	107356413	10,101718263,107356428	0,0,0
chr1	103478736	103478737	chr7	86260442	86260443	TRA	NA	+	+	[Svaba_SR=23,Svaba_PE=15],[Manta_PE=17,Manta_SR=18],[Lumpy_PE=12,Lumpy_SR=14]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC095032.1;DisruptR=;ClosestL=;ClosestR=	103478105	84789193	16,103478737,86260443	0,0,0
chr1	111229681	111229682	chr7	115766459	115766460	TRA	NA	-	-	[Manta_PE=4,Manta_SR=5]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CHI3L2;DisruptR=;ClosestL=;ClosestR=	107356413	116918672	0,0,0	0,0,0
chr1	124984581	124984582	chr21	15414727	15414728	TRA	NA	-	-	[Svaba_SR=7,Svaba_PE=9],[Manta_PE=7,Manta_SR=8]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=AJ009632.2;ClosestL=;ClosestR=	107356413	15873584	0,0,0	0,0,0
chr1	124984848	124984849	chr21	46035776	46035777	TRA	NA	+	-	[Svaba_SR=7,Svaba_PE=0],[Manta_PE=3,Manta_SR=7]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=AP001476.1	107356413	46107841	5,124984850,46035776	0,0,0
chr1	143191333	143191334	chr6	32039557	32039558	TRA	NA	+	+	[Svaba_SR=16,Svaba_PE=3],[Lumpy_PE=2,Lumpy_SR=3]	lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CYP21A2;ClosestL=;ClosestR=TNXB	150474851	32487100	10,143191335,32039559	0,0,0
chr1	150474819	150474820	chr1	150749754	150749755	DUP	NA	-	+	[Svaba_SR=55,Svaba_PE=53],[Manta_PE=42,Manta_SR=42],[Lumpy_PE=30,Lumpy_SR=35]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RPRD2;DisruptR=CTSS;ClosestL=TARS2;ClosestR=	150474851	150749712	36,150474821,150749755	0,0,0
chr1	150523171	150523172	chr6	21794803	21794804	TRA	NA	-	+	[Manta_PE=12,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CASC15;ClosestL=FALEC;ClosestR=	150474852	24909815	2,150522982,21794575	0,0,0
chr1	150980873	150980874	chr1	151012027	151012028	DEL	NA	+	-	[Manta_PE=7,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=PRUNE1;ClosestL=ANXA9;ClosestR=MINDY1	150749712	150749712	2,150980860,151012057	0,0,0
chr1	155287407	155287408	chr1	155310603	155310604	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=23],[Manta_PE=21,Manta_SR=15],[Lumpy_PE=15,Lumpy_SR=11]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=HCN3;DisruptR=FDPS;Fusion=HCN3+FDPS;ClosestL=PKLR;ClosestR=RUSC1-AS1	150749712	150749712	14,155287407,155310603	0,0,0
chr1	156727473	156727474	chr1	156728410	156728411	DEL	NA	+	-	[Svaba_SR=5,Svaba_PE=0],[Manta_PE=4,Manta_SR=6]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ISG20L2;DisruptR=ISG20L2;ClosestL=RRNAD1;ClosestR=RRNAD1	150749712	150749712	5,156727475,156728410	0,0,0
chr1	186672822	186672823	chr1	188617939	188617940	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=11],[Manta_PE=10,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PTGS2;DisruptR=;ClosestL=PACERR;ClosestR=	186672517	186672517	0,0,0	0,0,0
chr1	186672823	186672824	chr12	67114875	67114876	TRA	NA	-	+	[Svaba_SR=25,Svaba_PE=16],[Manta_PE=16,Manta_SR=19],[Lumpy_PE=11,Lumpy_SR=16]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PTGS2;DisruptR=;ClosestL=PACERR;ClosestR=RAB11AP2	186672517	67923115	17,186672823,67114876	0,0,0
chr1	188617781	188617782	chr21	32343522	32343523	TRA	NA	-	-	[Svaba_SR=25,Svaba_PE=6],[Manta_PE=5,Manta_SR=24],[Lumpy_PE=3,Lumpy_SR=18]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=URB1;ClosestL=;ClosestR=	186672517	32739659	21,188617781,32343522	0,0,0
chr1	188617939	188617940	chr12	67114681	67114682	TRA	NA	+	-	[Manta_PE=2,Manta_SR=18]	manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=RAB11AP2	186672517	67923115	17,188617941,67114681	0,0,0
chr1	188978471	188978472	chr12	28094082	28094083	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=10]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC01035;DisruptR=;ClosestL=;ClosestR=	186672517	41087	0,0,0	2,188978478,28094101
chr1	200173681	200173682	chr1	200175120	200175121	DEL	NA	+	-	[Svaba_SR=5,Svaba_PE=0]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=NR5A2;DisruptR=NR5A2;ClosestL=;ClosestR=	203360618	203360618	4,200173679,200175120	0,0,0
chr1	200899901	200899902	chr21	7949041	7949042	TRA	NA	-	+	[Svaba_SR=27,Svaba_PE=32]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=INAVA;DisruptR=;ClosestL=MROH3P;ClosestR=	203360618	13282812	19,200899900,7949042	0,0,0
chr1	200900232	200900233	chr10	29373569	29373570	TRA	NA	+	-	[Svaba_SR=40,Svaba_PE=12],[Manta_PE=12,Manta_SR=41]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=INAVA;DisruptR=;ClosestL=MROH3P;ClosestR=	203360618	29240716	20,200900233,29373569	0,0,0
chr1	200900232	200900233	chr5	164930879	164930880	TRA	NA	+	-	[Svaba_SR=60,Svaba_PE=30],[Manta_PE=27,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=INAVA;DisruptR=AC109466.1;Fusion=INAVA-AC109466.1;ClosestL=MROH3P;ClosestR=RNU6-209P	203360618	164930825	0,0,0	0,0,0
chr1	200908919	200908920	chr20	8765271	8765272	TRA	NA	-	-	[Svaba_SR=16,Svaba_PE=21],[Manta_PE=21,Manta_SR=10],[Lumpy_PE=20,Lumpy_SR=6]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=INAVA;DisruptR=PLCB1;ClosestL=MROH3P;ClosestR=	203360618	8764420	9,200908920,8765271	0,0,0
chr1	200934816	200934817	chr10	29240543	29240544	TRA	NA	+	+	[Svaba_SR=29,Svaba_PE=17],[Manta_PE=19,Manta_SR=24],[Lumpy_PE=13,Lumpy_SR=16]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MROH3P;DisruptR=;ClosestL=RNU6-704P;ClosestR=	203360618	29240715	18,200934818,29240547	0,0,0
chr1	202013942	202013943	chr1	202424227	202424228	DUP	NA	-	+	[Svaba_SR=29,Svaba_PE=33],[Manta_PE=29,Manta_SR=27],[Lumpy_PE=24,Lumpy_SR=16]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=ELF3|Tier2;DisruptL=ELF3,AL691482.3;DisruptR=PPP1R12B;Fusion=PPP1R12B+ELF3|PPP1R12B+AL691482.3;ClosestL=ELF3-AS1;ClosestR=RNU6-89P	203360618	203360618	21,202013942,202424228	0,0,0
chr1	202223003	202223004	chr1	202475925	202475926	DUP	NA	-	+	[Svaba_SR=20,Svaba_PE=24],[Manta_PE=26,Manta_SR=18],[Lumpy_PE=24,Lumpy_SR=9]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LGR6;DisruptR=PPP1R12B;Fusion=PPP1R12B+LGR6;ClosestL=;ClosestR=AC099336.2	203360618	203360618	6,202223006,202475926	0,0,0
chr1	203360676	203360677	chr1	223431545	223431546	DUP	NA	-	+	[Svaba_SR=82,Svaba_PE=106],[Manta_PE=101,Manta_SR=76],[Lumpy_PE=88,Lumpy_SR=57]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=SLC45A3|Tier1,MDM4|Tier1,ELK4|Tier1;DisruptL=;DisruptR=;ClosestL=AL359837.1;ClosestR=	203360619	223431463	53,203360677,223431549	0,0,0
chr1	203425428	203425429	chr1	203429109	203429110	INV	NA	+	+	[Svaba_SR=17,Svaba_PE=25],[Manta_PE=28,Manta_SR=14],[Lumpy_PE=26,Lumpy_SR=10]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	203360619	203360619	2,203425427,203429110	0,0,0
chr1	205097876	205097877	chr1	235138998	235138999	DEL	NA	+	-	[Svaba_SR=29,Svaba_PE=32],[Manta_PE=26,Manta_SR=29],[Lumpy_PE=17,Lumpy_SR=20]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=SLC45A3|Tier1,ELK4|Tier1,H3F3A|Tier1;DisruptL=RBBP5;DisruptR=RBM34,ARID4B;Fusion=RBM34+RBBP5|ARID4B+RBBP5;ClosestL=AL583832.1;ClosestR=TOMM20	205097487	234776418	16,205097891,235138998	0,0,0
chr1	209171311	209171312	chr13	108157081	108157082	TRA	NA	+	+	[Svaba_SR=28,Svaba_PE=23],[Manta_PE=23,Manta_SR=25],[Lumpy_PE=17,Lumpy_SR=16]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC092810.2;ClosestR=	212301736	107326495	22,209171312,108157082	0,0,0
chr1	209244791	209244792	chr1	212681433	212681434	DUP	NA	-	+	[Svaba_SR=15,Svaba_PE=26],[Manta_PE=25,Manta_SR=12],[Lumpy_PE=24,Lumpy_SR=6]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=AC092810.1;ClosestR=BATF3	212301736	213004741	2,209244790,212681443	0,0,0
chr1	211388560	211388561	chr2	104320969	104320970	TRA	NA	-	-	[Svaba_SR=19,Svaba_PE=16],[Manta_PE=18,Manta_SR=20],[Lumpy_PE=10,Lumpy_SR=14]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC00467;DisruptR=;ClosestL=TRAF5;ClosestR=	212301736	105664599	17,211388547,104320969	0,0,0
chr1	211808734	211808735	chr19	14950825	14950826	TRA	NA	+	+	[Svaba_SR=17,Svaba_PE=23],[Manta_PE=21,Manta_SR=14],[Lumpy_PE=13,Lumpy_SR=13]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LPGAT1;DisruptR=SLC1A6;ClosestL=RF00019;ClosestR=OR7C2	212301736	14687524	12,211808735,14950826	0,0,0
chr1	212301721	212301722	chr6	30029837	30029838	TRA	NA	-	-	[Svaba_SR=70,Svaba_PE=83],[Manta_PE=91,Manta_SR=61],[Lumpy_PE=60,Lumpy_SR=48]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AL360091.3,PPP2R5A;DisruptR=ZNRD1ASP;Fusion=ZNRD1ASP-PPP2R5A;ClosestL=AL360091.2;ClosestR=ETF1P1	212301736	32487100	45,212301724,30029837	0,0,0
chr1	213000165	213000166	chr8	121698470	121698471	TRA	NA	+	-	[Svaba_SR=15,Svaba_PE=14],[Manta_PE=14,Manta_SR=11],[Lumpy_PE=10,Lumpy_SR=8]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ANGEL2;DisruptR=AC104233.1;ClosestL=VASH2;ClosestR=AC104233.2	213004741	121696691	11,213000167,121698468	0,0,0
chr1	217777448	217777449	chr11	29804982	29804983	TRA	NA	-	+	[Svaba_SR=34,Svaba_PE=36],[Manta_PE=31,Manta_SR=29],[Lumpy_PE=23,Lumpy_SR=23]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SPATA17;DisruptR=AC107973.1;Fusion=AC107973.1-SPATA17;ClosestL=SPATA17-AS1;ClosestR=	217777418	29804998	26,217777448,29804983	0,0,0
chr1	220803994	220803995	chrX	87103995	87103996	TRA	NA	-	-	[Svaba_SR=13,Svaba_PE=11],[Manta_PE=11,Manta_SR=12],[Lumpy_PE=5,Lumpy_SR=12]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MARC1;DisruptR=;ClosestL=MARC2;ClosestR=	220805315	87101847	10,220803997,87103995	0,0,0
chr1	221676688	221676689	chr7	140930514	140930515	TRA	NA	-	+	[Svaba_SR=16,Svaba_PE=15],[Manta_PE=17,Manta_SR=11],[Lumpy_PE=15,Lumpy_SR=7]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=AC006006.1	220805316	137445254	11,221676690,140930515	0,0,0
chr1	222787229	222787230	chr1	222795328	222795329	INV	NA	+	+	[Svaba_SR=25,Svaba_PE=25],[Manta_PE=23,Manta_SR=23],[Lumpy_PE=18,Lumpy_SR=21]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=AL392172.1	223431462	223431462	20,222787229,222795329	0,0,0
chr1	222794716	222794717	chr18	73989233	73989234	TRA	NA	-	-	[Svaba_SR=23,Svaba_PE=25],[Manta_PE=29,Manta_SR=19],[Lumpy_PE=20,Lumpy_SR=15]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=AC090125.1;ClosestL=;ClosestR=	223431462	73989169	17,222794718,73989233	0,0,0
chr1	234957883	234957884	chr1	235095124	235095125	DUP	NA	-	+	[Svaba_SR=16,Svaba_PE=20],[Manta_PE=18,Manta_SR=14],[Lumpy_PE=15,Lumpy_SR=11]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AL391832.1,AL391832.2;DisruptR=;ClosestL=;ClosestR=AL732292.1	234776418	234776418	10,234957886,235095125	0,0,0
chr1	234972979	234972980	chr1	235146066	235146067	DUP	NA	-	+	[Svaba_SR=30,Svaba_PE=36],[Manta_PE=35,Manta_SR=26],[Lumpy_PE=25,Lumpy_SR=16]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=RBM34,ARID4B;ClosestL=AL391832.2;ClosestR=TOMM20	234776418	234776418	2,234972981,235146066	0,0,0
chr1	246598539	246598540	chr1	246600082	246600083	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=22],[Manta_PE=23,Manta_SR=17],[Lumpy_PE=16,Lumpy_SR=15]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CNST;DisruptR=CNST;ClosestL=AL591623.1;ClosestR=AL591623.1	248946322	248946322	12,246598539,246600082	0,0,0
chr2	1524653	1524654	chr2	1525431	1525432	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TPO;DisruptR=TPO;ClosestL=;ClosestR=	10005	10005	0,0,0	0,0,0
chr2	2752746	2752747	chr6	52542329	52542330	TRA	NA	-	-	[Svaba_SR=23,Svaba_PE=15],[Manta_PE=9,Manta_SR=20],[Lumpy_PE=7,Lumpy_SR=14]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=TRAM2;ClosestL=;ClosestR=EFHC1	10005	52679253	16,2752747,52542329	0,0,0
chr2	2752961	2752962	chr14	102959581	102959582	TRA	NA	+	+	[Manta_PE=3,Manta_SR=20]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CDC42BPB;ClosestL=;ClosestR=	10005	104243063	10,2752963,102959582	0,0,0
chr2	2752962	2752963	chr17	35740374	35740375	TRA	NA	+	+	[Svaba_SR=39,Svaba_PE=4]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=;ClosestR=GAS2L2	10005	36041470	0,0,0	0,0,0
chr2	2752962	2752963	chr2	91414359	91414360	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=10],[Manta_PE=9,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=MYCN|Tier1,PCBP1|Tier2,C2orf44|Tier1,NCOA1|Tier1,ASXL2|Tier2,SIX2|Tier2,EPAS1|Tier1,MSH6|Tier1,FBXO11|Tier1,BCL11A|Tier1,REL|Tier1,XPO1|Tier1,DCTN1|Tier1,DNMT3A|Tier1,STRN|Tier1,EML4|Tier1,MSH2|Tier1,ALK|Tier1,BIRC6|Tier2;DisruptL=;DisruptR=;ClosestL=;ClosestR=	10005	94141931	0,0,0	0,0,0
chr2	20726878	20726879	chr2	20774844	20774845	DEL	NA	+	-	[Svaba_SR=11,Svaba_PE=12],[Manta_PE=11,Manta_SR=10],[Lumpy_PE=7,Lumpy_SR=7]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LDAH;DisruptR=LDAH;ClosestL=;ClosestR=	37825578	37825578	9,20726880,20774844	0,0,0
chr2	24579528	24579529	chr2	24695351	24695352	DUP	NA	-	+	[Svaba_SR=18,Svaba_PE=31],[Manta_PE=31,Manta_SR=13],[Lumpy_PE=23,Lumpy_SR=12]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=NCOA1|Tier1;DisruptL=NCOA1;DisruptR=NCOA1;ClosestL=RNA5SP88;ClosestR=RNU6-936P	37825578	37825578	11,24579529,24695352	0,0,0
chr2	33705112	33705113	chr2	33705891	33705892	DEL	NA	+	-	[Svaba_SR=5,Svaba_PE=0],[Manta_PE=2,Manta_SR=5],[Lumpy_PE=4,Lumpy_SR=4]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=LINC01317;ClosestR=LINC01317	37825578	37825578	5,33705113,33705891	0,0,0
chr2	37825636	37825637	chr17	72487322	72487323	TRA	NA	-	-	[Svaba_SR=14,Svaba_PE=20],[Manta_PE=20,Manta_SR=12],[Lumpy_PE=14,Lumpy_SR=10]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=LINC00511;ClosestL=LINC00211;ClosestR=	37825579	67102560	10,37825628,72487320	0,0,0
chr2	62620842	62620843	chr2	63261205	63261206	DUP	NA	-	+	[Svaba_SR=37,Svaba_PE=40],[Manta_PE=33,Manta_SR=27],[Lumpy_PE=31,Lumpy_SR=2]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AC092155.1;DisruptR=WDPCP;Fusion=AC092155.1+WDPCP;ClosestL=;ClosestR=	62620851	63608437	0,0,0	0,0,0
chr2	63034488	63034489	chr13	16683888	16683889	TRA	NA	-	+	[Svaba_SR=12,Svaba_PE=14],[Manta_PE=8,Manta_SR=21],[Lumpy_PE=5,Lumpy_SR=2]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=EHBP1;DisruptR=;ClosestL=AC009501.1;ClosestR=	62620851	16000006	20,63034489,16683889	0,0,0
chr2	91414360	91414361	chr14	102959495	102959496	TRA	NA	-	-	[Manta_PE=0,Manta_SR=24]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CDC42BPB;ClosestL=;ClosestR=	94141931	104243063	8,91414360,102959494	0,0,0
chr2	91414462	91414463	chr17	35740374	35740375	TRA	NA	+	+	[Svaba_SR=16,Svaba_PE=0],[Manta_PE=3,Manta_SR=18],[Lumpy_PE=3,Lumpy_SR=12]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=;ClosestR=GAS2L2	94141931	36041470	11,91414462,35740375	0,0,0
chr2	96997335	96997336	chr11	73060366	73060367	TRA	NA	+	+	[Svaba_SR=19,Svaba_PE=18],[Manta_PE=19,Manta_SR=13],[Lumpy_PE=14,Lumpy_SR=9]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=FCHSD2;ClosestL=AC079395.3;ClosestR=	95642457	73059915	13,96997336,73060367	0,0,0
chr2	99435882	99435883	chr2	103741228	103741229	INV	NA	-	-	[Lumpy_PE=3,Lumpy_SR=2]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=AFF3|Tier1;DisruptL=REV1;DisruptR=;ClosestL=;ClosestR=	95642457	105664599	2,99435880,103741227	0,0,0
chr2	99500341	99500342	chr2	101098846	101098847	DEL	NA	+	-	[Svaba_SR=5,Svaba_PE=5],[Manta_PE=5,Manta_SR=5],[Lumpy_PE=5,Lumpy_SR=2]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=AFF3|Tier1;DisruptL=;DisruptR=TBC1D8;ClosestL=REV1;ClosestR=	95642457	105664599	2,99500343,101098846	0,0,0
chr2	99677001	99677002	chr22	24803524	24803525	TRA	NA	-	+	[Svaba_SR=22,Svaba_PE=23],[Manta_PE=21,Manta_SR=20],[Lumpy_PE=8,Lumpy_SR=17]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=AFF3|Tier1;DisruptL=AFF3;DisruptR=;ClosestL=;ClosestR=SGSM1	95642457	24015969	17,99677001,24803525	0,0,0
chr2	99696052	99696053	chr2	99745352	99745353	INV	NA	+	+	[Svaba_SR=13,Svaba_PE=10],[Manta_PE=12,Manta_SR=13],[Lumpy_PE=10,Lumpy_SR=11]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=AFF3|Tier1;DisruptL=AFF3;DisruptR=AFF3;ClosestL=;ClosestR=	95642457	95642457	8,99696052,99745353	0,0,0
chr2	100094211	100094212	chr2	104093618	104093619	INV	NA	-	-	[Manta_PE=1,Manta_SR=9]	manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=AFF3|Tier1;DisruptL=AFF3;DisruptR=;ClosestL=AC092667.1;ClosestR=LINC01965	95642457	105664599	8,100094213,104093617	0,0,0
chr2	101119638	101119639	chr10	38528505	38528506	TRA	NA	-	-	[Svaba_SR=21,Svaba_PE=28],[Lumpy_PE=19,Lumpy_SR=17]	lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TBC1D8;DisruptR=;ClosestL=;ClosestR=	105664599	39580116	13,101119642,38528505	0,0,0
chr2	101119899	101119900	chr10	38527881	38527882	TRA	NA	+	-	[Svaba_SR=16,Svaba_PE=26],[Lumpy_PE=15,Lumpy_SR=8]	svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TBC1D8;DisruptR=;ClosestL=;ClosestR=	105664599	39580116	5,101119900,38527881	0,0,0
chr2	101672710	101672711	chr10	38925624	38925625	TRA	NA	-	+	[Lumpy_PE=2,Lumpy_SR=2]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	105664599	39580116	4,101672713,38925624	0,0,0
chr2	103110745	103110746	chr2	103111960	103111961	INV	NA	+	+	[Svaba_SR=19,Svaba_PE=16],[Manta_PE=21,Manta_SR=17],[Lumpy_PE=14,Lumpy_SR=16]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC073987.1;DisruptR=AC073987.1;ClosestL=;ClosestR=	105664599	105664599	12,103110745,103111961	0,0,0
chr2	103221167	103221168	chr2	103222714	103222715	DUP	NA	-	+	[Manta_PE=3,Manta_SR=4],[Lumpy_PE=3,Lumpy_SR=3]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	105664599	105664599	3,103221169,103222717	0,0,0
chr2	103221390	103221391	chr2	103221966	103221967	INV	NA	+	+	[Manta_PE=6,Manta_SR=2],[Lumpy_PE=6,Lumpy_SR=2]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	105664599	105664599	2,103221392,103221967	0,0,0
chr2	104061834	104061835	chr22	49964192	49964193	TRA	NA	-	+	[Svaba_SR=18,Svaba_PE=23],[Manta_PE=19,Manta_SR=12],[Lumpy_PE=17,Lumpy_SR=6]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC01965;DisruptR=;ClosestL=;ClosestR=PIM3	105664599	50808368	8,104061833,49964193	0,0,0
chr2	104063183	104063184	chr22	49963830	49963831	TRA	NA	-	-	[Svaba_SR=15,Svaba_PE=9],[Manta_PE=10,Manta_SR=10],[Lumpy_PE=7,Lumpy_SR=8]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC01965;DisruptR=PIM3;ClosestL=;ClosestR=MIR6821	105664599	50808368	10,104063183,49963830	0,0,0
chr2	104240194	104240195	chr16	465006	465007	TRA	NA	+	-	[Svaba_SR=35,Svaba_PE=42],[Manta_PE=39,Manta_SR=28],[Lumpy_PE=29,Lumpy_SR=20]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=RAB11FIP3;ClosestL=;ClosestR=AL049542.1	105664599	10005	26,104240194,465006	0,0,0
chr2	109290685	109290686	chr18	24684289	24684290	TRA	NA	-	+	[Svaba_SR=18,Svaba_PE=26],[Manta_PE=24,Manta_SR=14],[Lumpy_PE=16,Lumpy_SR=11]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SH3RF3;DisruptR=;ClosestL=;ClosestR=RAC1P1	109199785	24683978	12,109290684,24684291	0,0,0
chr2	114725269	114725270	chr18	63805018	63805019	TRA	NA	+	-	[Svaba_SR=19,Svaba_PE=16],[Manta_PE=15,Manta_SR=18],[Lumpy_PE=10,Lumpy_SR=13]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=DPP10;DisruptR=SERPINB7;Fusion=DPP10-SERPINB7;ClosestL=;ClosestR=	114973555	61626460	14,114725273,63805017	0,0,0
chr2	114974129	114974130	chr21	32740681	32740682	TRA	NA	+	+	[Svaba_SR=27,Svaba_PE=24],[Manta_PE=24,Manta_SR=23],[Lumpy_PE=17,Lumpy_SR=17]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=DPP10;DisruptR=PAXBP1-AS1,PAXBP1;Fusion=DPP10-PAXBP1;ClosestL=;ClosestR=SYNJ1	114973556	32739660	17,114974128,32740689	0,0,0
chr2	115753434	115753435	chr22	28670132	28670133	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=11],[Manta_PE=9,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=DPP10;DisruptR=TTC28;ClosestL=;ClosestR=CHEK2	114973556	29344638	0,0,0	0,0,0
chr2	115753450	115753451	chr22	28669982	28669983	TRA	NA	+	-	[Svaba_SR=13,Svaba_PE=0],[Manta_PE=4,Manta_SR=7]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=DPP10;DisruptR=TTC28;ClosestL=;ClosestR=CHEK2	114973556	29344638	6,115753450,28669982	0,0,0
chr2	135367225	135367226	chr2	135375203	135375204	DEL	NA	+	-	[Svaba_SR=43,Svaba_PE=50],[Manta_PE=46,Manta_SR=37],[Lumpy_PE=32,Lumpy_SR=31]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ZRANB3;DisruptR=ZRANB3;ClosestL=;ClosestR=	114973556	114973556	29,135367224,135375203	0,0,0
chr2	142877181	142877182	chr2	142883247	142883248	DEL	NA	+	-	[Svaba_SR=19,Svaba_PE=24],[Manta_PE=23,Manta_SR=20],[Lumpy_PE=14,Lumpy_SR=10]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=KYNU;ClosestL=KYNU;ClosestR=	114973556	114973556	16,142877187,142883246	0,0,0
chr2	143042583	143042584	chr12	30577021	30577022	TRA	NA	-	+	[Lumpy_PE=4,Lumpy_SR=1]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=KYNU;DisruptR=;ClosestL=;ClosestR=	114973556	56255606	3,143042582,30577008	0,0,0
chr2	152347817	152347818	chr2	152457171	152457172	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=31],[Manta_PE=26,Manta_SR=19],[Lumpy_PE=20,Lumpy_SR=16]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=FMNL2;DisruptR=FMNL2;ClosestL=;ClosestR=	114973556	114973556	16,152347818,152457171	0,0,0
chr2	154517952	154517953	chr7	135096610	135096611	TRA	NA	-	-	[Manta_PE=0,Manta_SR=18]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=AGBL3,CYREN;ClosestL=;ClosestR=	114973556	137445253	0,0,0	0,0,0
chr2	165399970	165399971	chr2	166129437	166129438	DUP	NA	-	+	[Svaba_SR=36,Svaba_PE=33],[Manta_PE=34,Manta_SR=29],[Lumpy_PE=24,Lumpy_SR=21]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=AC010127.1,SCN1A;ClosestL=SCN2A;ClosestR=RF00019	114973556	114973556	28,165399973,166129438	0,0,0
chr2	179388075	179388076	chrX	4728353	4728354	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=40],[Manta_PE=22,Manta_SR=25]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC068042.1;ClosestR=	242183395	10446	0,0,0	0,0,0
chr2	179388334	179388335	chrX	4728528	4728529	TRA	NA	-	+	[Svaba_SR=53,Svaba_PE=46],[Manta_PE=39,Manta_SR=45],[Lumpy_PE=27,Lumpy_SR=17]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC068042.1;ClosestR=	242183395	10446	33,179388337,4728529	0,0,0
chr2	187258585	187258586	chr11	69848700	69848701	TRA	NA	+	-	[Manta_PE=7,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC007319.1;DisruptR=;ClosestL=RNU6-989P;ClosestR=	242183395	69779347	9,187258376,69848604	2,187258353,69848597
chr2	187552041	187552042	chr2	187556879	187556880	DEL	NA	+	-	[Svaba_SR=11,Svaba_PE=17],[Manta_PE=12,Manta_SR=17],[Lumpy_PE=7,Lumpy_SR=8]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC007319.1,TFPI;DisruptR=TFPI;ClosestL=;ClosestR=AC007319.1	242183395	242183395	11,187552043,187556879	0,0,0
chr2	188399228	188399229	chr5	59193764	59193765	TRA	NA	+	-	[Svaba_SR=8,Svaba_PE=2],[Manta_PE=2,Manta_SR=8],[Lumpy_PE=2,Lumpy_SR=4]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=GULP1;DisruptR=PDE4D;ClosestL=LINC01090;ClosestR=	242183395	32366973	4,188399230,59193764	0,0,0
chr2	218087110	218087111	chr2	218098245	218098246	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=23],[Manta_PE=21,Manta_SR=14],[Lumpy_PE=13,Lumpy_SR=9]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RUFY4;DisruptR=;ClosestL=;ClosestR=RUFY4	242183395	242183395	12,218087112,218098245	0,0,0
chr3	9307908	9307909	chr3	9404959	9404960	DUP	NA	-	+	[Svaba_SR=49,Svaba_PE=63],[Manta_PE=58,Manta_SR=48],[Lumpy_PE=55,Lumpy_SR=22]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SRGAP3,AC026191.1;DisruptR=SETD5;ClosestL=;ClosestR=THUMPD3-AS1	9676603	9676603	0,0,0	0,0,0
chr3	9676589	9676590	chr3	10083212	10083213	DUP	NA	-	+	[Svaba_SR=70,Svaba_PE=79],[Manta_PE=74,Manta_SR=60],[Lumpy_PE=66,Lumpy_SR=34]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=FANCD2|Tier1;DisruptL=MTMR14;DisruptR=FANCD2,FANCD2OS;Fusion=FANCD2+MTMR14;ClosestL=;ClosestR=	9676603	10083194	46,9676588,10083213	0,0,0
chr3	13545519	13545520	chr17	35740201	35740202	TRA	NA	-	-	[Svaba_SR=31,Svaba_PE=2]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=FBLN2;ClosestR=GAS2L2	10083194	36041470	0,0,0	0,0,0
chr3	13545519	13545520	chr9	72457733	72457734	TRA	NA	-	-	[Svaba_SR=21,Svaba_PE=15],[Manta_PE=15,Manta_SR=20],[Lumpy_PE=11,Lumpy_SR=12]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=FBLN2;ClosestR=AL445646.1	10083194	66040022	14,13545512,72457733	0,0,0
chr3	13545970	13545971	chr21	32343657	32343658	TRA	NA	+	+	[Svaba_SR=30,Svaba_PE=11],[Manta_PE=10,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=URB1;ClosestL=FBLN2;ClosestR=	10083194	32739659	0,0,0	0,0,0
chr3	13545970	13545971	chr6	144660231	144660232	TRA	NA	+	-	[Svaba_SR=19,Svaba_PE=5],[Manta_PE=6,Manta_SR=15],[Lumpy_PE=2,Lumpy_SR=12]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=UTRN;ClosestL=FBLN2;ClosestR=	10083194	130003967	11,13545972,144660225	0,0,0
chr3	37547039	37547040	chr3	37719792	37719793	DUP	NA	-	+	[Svaba_SR=52,Svaba_PE=60],[Manta_PE=51,Manta_SR=47],[Lumpy_PE=44,Lumpy_SR=37]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ITGA9;DisruptR=ITGA9;ClosestL=;ClosestR=	37547021	37719800	37,37547042,37719793	0,0,0
chr3	39770252	39770253	chr3	41312690	41312691	DUP	NA	-	+	[Svaba_SR=63,Svaba_PE=70],[Manta_PE=65,Manta_SR=51],[Lumpy_PE=60,Lumpy_SR=40]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=CTNNB1|Tier1;DisruptL=;DisruptR=ULK4;ClosestL=;ClosestR=	39770243	41312676	40,39770256,41312691	0,0,0
chr3	41158029	41158030	chr14	100903975	100903976	TRA	NA	+	+	[Svaba_SR=18,Svaba_PE=10],[Manta_PE=7,Manta_SR=20],[Lumpy_PE=3,Lumpy_SR=15]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=AL117190.1,MEG8;ClosestL=AC009743.1;ClosestR=RF02146	41312675	104243063	12,41158031,100903976	0,0,0
chr3	41158029	41158030	chrX	87668584	87668585	TRA	NA	+	-	[Svaba_SR=29,Svaba_PE=10]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=KLHL4;ClosestL=AC009743.1;ClosestR=	41312675	87101847	0,0,0	0,0,0
chr3	52565285	52565286	chr3	52629472	52629473	DEL	NA	+	-	[Svaba_SR=44,Svaba_PE=50],[Manta_PE=48,Manta_SR=36],[Lumpy_PE=37,Lumpy_SR=18]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=PBRM1|Tier1;DisruptL=SMIM4,PBRM1;DisruptR=PBRM1;ClosestL=RNU6ATAC16P;ClosestR=	52565238	52629454	17,52565284,52629472	0,0,0
chr3	77731108	77731109	chr5	22675663	22675664	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CDH12;ClosestL=;ClosestR=	85183422	32366972	2,77731164,22675887	0,0,0
chr3	85183520	85183521	chr3	85187151	85187152	INV	NA	-	-	[Svaba_SR=44,Svaba_PE=0],[Manta_PE=40,Manta_SR=44],[Lumpy_PE=29,Lumpy_SR=26]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CADM2;DisruptR=CADM2;ClosestL=;ClosestR=	85183423	85183423	32,85183519,85187151	0,0,0
chr3	85660778	85660779	chr3	85663710	85663711	DEL	NA	+	-	[Svaba_SR=40,Svaba_PE=48],[Manta_PE=42,Manta_SR=33],[Lumpy_PE=29,Lumpy_SR=27]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CADM2;DisruptR=CADM2;ClosestL=;ClosestR=	85183423	85183423	26,85660777,85663710	0,0,0
chr3	85831779	85831780	chrX	80286854	80286855	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=13]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CADM2;DisruptR=CHMP1B2P;Fusion=CADM2-CHMP1B2P;ClosestL=CADM2-AS2;ClosestR=	85183423	76245724	0,0,0	0,0,0
chr3	91672220	91672221	chr3	95006137	95006138	DUP	NA	-	+	[Svaba_SR=8,Svaba_PE=0]	svaba	HCC-1143_80--HCC-1143BL_40	known=;gap;DisruptL=;DisruptR=LINC00879;ClosestL=;ClosestR=	93455911	95005471	10,91672224,95006138	0,0,0
chr3	94678278	94678279	chr10	61749704	61749705	TRA	NA	-	-	[Manta_PE=4,Manta_SR=4]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CABCOCO1;ClosestL=;ClosestR=	95005470	63904755	3,94678277,61749704	0,0,0
chr3	95900220	95900221	chr5	153304740	153304741	TRA	NA	+	-	[Manta_PE=4,Manta_SR=5]	manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	95005471	164930824	4,95900222,153304739	0,0,0
chr3	117319407	117319408	chr3	117323182	117323183	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=17],[Manta_PE=13,Manta_SR=22],[Lumpy_PE=9,Lumpy_SR=17]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	95005471	95005471	19,117319408,117323182	0,0,0
chr3	126089031	126089032	chr3	126135677	126135678	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=19],[Manta_PE=17,Manta_SR=19],[Lumpy_PE=13,Lumpy_SR=12]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SLC41A3,AC079848.1;DisruptR=ALDH1L1;Fusion=ALDH1L1+SLC41A3;ClosestL=ALDH1L1;ClosestR=	95005471	95005471	15,126089033,126135677	0,0,0
chr3	132552072	132552073	chr21	16887338	16887339	TRA	NA	+	-	[Manta_PE=3,Manta_SR=5],[Lumpy_PE=2,Lumpy_SR=2]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=ACAD11;ClosestR=AF212831.1	95005471	17474345	4,132552074,16887338	0,0,0
chr3	141665762	141665763	chr17	73289754	73289755	TRA	NA	-	+	[Manta_PE=0,Manta_SR=22]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC092978.1;DisruptR=CDC42EP4;ClosestL=;ClosestR=	170316551	67102560	6,141665769,73289763	0,0,0
chr3	156596536	156596537	chr20	22251588	22251589	TRA	NA	-	-	[Svaba_SR=15,Svaba_PE=7],[Manta_PE=8,Manta_SR=15],[Lumpy_PE=8,Lumpy_SR=3]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=LINC01427	170316551	21885645	15,156596535,22251588	0,0,0
chr3	156596713	156596714	chr20	22253039	22253040	TRA	NA	+	-	[Svaba_SR=14,Svaba_PE=8],[Manta_PE=5,Manta_SR=11],[Lumpy_PE=4,Lumpy_SR=5]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=LINC01427	170316551	21885645	10,156596713,22253039	0,0,0
chr3	168845996	168845997	chr3	168846503	168846504	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=RPL21P43;ClosestR=RPL21P43	170316551	170316551	0,0,0	0,0,0
chr3	170317088	170317089	chr3	195524531	195524532	INV	NA	-	-	[Svaba_SR=24,Svaba_PE=29],[Manta_PE=28,Manta_SR=19],[Lumpy_PE=18,Lumpy_SR=16]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=SOX2|Tier1,EIF4A2|Tier1,TBL1XR1|Tier1,PIK3CA|Tier1,ETV5|Tier1,BCL6|Tier1,MAP3K13|Tier1,IGF2BP2|Tier2,MB21D2|Tier2,LPP|Tier1,TP63|Tier1;DisruptL=;DisruptR=PPP1R2;ClosestL=PRKCI;ClosestR=RNU6ATAC24P	170316552	194248004	17,170317087,195524531	0,0,0
chr3	173507699	173507700	chr3	195524477	195524478	INV	NA	+	+	[Svaba_SR=25,Svaba_PE=27],[Manta_PE=25,Manta_SR=20],[Lumpy_PE=22,Lumpy_SR=12]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=SOX2|Tier1,EIF4A2|Tier1,TBL1XR1|Tier1,PIK3CA|Tier1,ETV5|Tier1,BCL6|Tier1,MAP3K13|Tier1,IGF2BP2|Tier2,MB21D2|Tier2,LPP|Tier1,TP63|Tier1;DisruptL=NLGN1;DisruptR=PPP1R2;Fusion=NLGN1+PPP1R2;ClosestL=;ClosestR=RNU6ATAC24P	173659062	194248004	17,173507699,195524478	0,0,0
chr3	173507997	173507998	chr3	194247718	194247719	INV	NA	-	-	[Svaba_SR=22,Svaba_PE=23],[Manta_PE=23,Manta_SR=20],[Lumpy_PE=17,Lumpy_SR=9]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SOX2|Tier1,EIF4A2|Tier1,TBL1XR1|Tier1,PIK3CA|Tier1,ETV5|Tier1,BCL6|Tier1,MAP3K13|Tier1,IGF2BP2|Tier2,MB21D2|Tier2,LPP|Tier1,TP63|Tier1;DisruptL=NLGN1;DisruptR=LINC02036,LINC02037;Fusion=LINC02036+NLGN1;ClosestL=;ClosestR=	173659062	194248003	0,0,0	0,0,0
chr3	179805191	179805192	chr7	44078620	44078621	TRA	NA	-	+	[Manta_PE=7,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PEX5L;DisruptR=POLM;Fusion=PEX5L-POLM;ClosestL=AC007687.1;ClosestR=MIR6838	173659063	43477639	0,0,0	0,0,0
chr3	183359824	183359825	chr5	139904003	139904004	TRA	NA	-	-	[Manta_PE=8,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MCF2L2;DisruptR=NRG2;ClosestL=;ClosestR=	173659063	164930824	0,0,0	0,0,0
chr3	193906127	193906128	chr3	193912491	193912492	DEL	NA	+	-	[Svaba_SR=45,Svaba_PE=59],[Manta_PE=61,Manta_SR=34]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	194248003	194248003	23,193906127,193912491	0,0,0
chr4	7325452	7325453	chr10	51033383	51033384	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=13],[Manta_PE=9,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=SORCS2-PRKG1;ClosestL=MIR4798;ClosestR=	10011	39580117	0,0,0	0,0,0
chr4	7325452	7325453	chr10	51033894	51033895	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=13]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=SORCS2-PRKG1;ClosestL=MIR4798;ClosestR=	10011	39580117	0,0,0	0,0,0
chr4	7325452	7325453	chr10	51269343	51269344	TRA	NA	+	-	[Svaba_SR=69,Svaba_PE=56],[Manta_PE=55,Manta_SR=58],[Lumpy_PE=37,Lumpy_SR=48]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=SORCS2-PRKG1;ClosestL=MIR4798;ClosestR=	10011	39580117	45,7325452,51269343	0,0,0
chr4	7334743	7334744	chr10	50991309	50991310	TRA	NA	-	+	[Svaba_SR=73,Svaba_PE=100],[Manta_PE=86,Manta_SR=63],[Lumpy_PE=60,Lumpy_SR=54]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=PRKG1-SORCS2;ClosestL=;ClosestR=	10011	39580117	44,7334745,50991310	0,0,0
chr4	13541213	13541214	chr4	13542655	13542656	DEL	NA	+	-	[Svaba_SR=14,Svaba_PE=19],[Manta_PE=18,Manta_SR=12],[Lumpy_PE=11,Lumpy_SR=10]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=NKX3-2;DisruptR=NKX3-2;ClosestL=LINC01096;ClosestR=LINC01096	14827697	14827697	10,13541212,13542655	0,0,0
chr4	14827425	14827426	chr4	15665086	15665087	DUP	NA	-	+	[Svaba_SR=30,Svaba_PE=33],[Manta_PE=31,Manta_SR=26],[Lumpy_PE=25,Lumpy_SR=20]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC00504;DisruptR=FBXL5;Fusion=LINC00504+FBXL5;ClosestL=;ClosestR=FAM200B	14827697	15664844	22,14827427,15665087	0,0,0
chr4	22959992	22959993	chr4	22967233	22967234	DEL	NA	+	-	[Svaba_SR=59,Svaba_PE=66],[Manta_PE=63,Manta_SR=48],[Lumpy_PE=45,Lumpy_SR=33]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;ClosestL=;ClosestR=	15664844	15664844	38,22959992,22967233	0,0,0
chr4	37747941	37747942	chr4	37749092	37749093	DEL	NA	+	-	[Svaba_SR=15,Svaba_PE=17],[Manta_PE=11,Manta_SR=14],[Lumpy_PE=10,Lumpy_SR=12]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	52771714	52771714	11,37747943,37749088	0,0,0
chr4	41713489	41713490	chr4	41722276	41722277	DEL	NA	+	-	[Svaba_SR=18,Svaba_PE=20],[Manta_PE=21,Manta_SR=20],[Lumpy_PE=16,Lumpy_SR=10]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=OR5M14P;ClosestR=OR5M14P	52771714	52771714	16,41713489,41722276	0,0,0
chr4	53357081	53357082	chr20	31572616	31572617	TRA	NA	-	-	[Lumpy_PE=3,Lumpy_SR=1]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SCFD2;DisruptR=HM13,HM13-AS1;Fusion=SCFD2-HM13;ClosestL=;ClosestR=AL110115.2	52771742	31539739	0,0,0	0,0,0
chr4	54132841	54132842	chr4	54134550	54134551	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=32],[Manta_PE=30,Manta_SR=18],[Lumpy_PE=21,Lumpy_SR=13]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC058822.1;DisruptR=AC058822.1;ClosestL=;ClosestR=	52771742	52771742	14,54132841,54134550	0,0,0
chr4	57019050	57019051	chr7	56443992	56443993	TRA	NA	-	-	[Svaba_SR=19,Svaba_PE=19],[Manta_PE=20,Manta_SR=18],[Lumpy_PE=16,Lumpy_SR=14]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=POLR2B;DisruptR=AC092447.7;Fusion=AC092447.7-POLR2B;ClosestL=IGFBP7;ClosestR=AC092447.10	57339073	57487363	18,57019050,56443992	0,0,0
chr4	59828040	59828041	chr4	59828615	59828616	DEL	NA	+	-	[Manta_PE=66,Manta_SR=82],[Lumpy_PE=60,Lumpy_SR=57]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=RF00019;ClosestR=RF00019	59832563	59832563	55,59828042,59828616	0,0,0
chr4	59832640	59832641	chr9	28551943	28551944	TRA	NA	+	-	[Svaba_SR=85,Svaba_PE=93],[Manta_PE=82,Manta_SR=75],[Lumpy_PE=57,Lumpy_SR=57]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=LINGO2;ClosestL=RF00019;ClosestR=	59832564	28551865	52,59832641,28551943	0,0,0
chr4	65266722	65266723	chr11	69365928	69365929	TRA	NA	+	-	[Svaba_SR=77,Svaba_PE=104],[Manta_PE=93,Manta_SR=71],[Lumpy_PE=70,Lumpy_SR=60]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=MYEOV;ClosestL=;ClosestR=AP005233.2	65266705	69098162	53,65266721,69365928	0,0,0
chr4	82823868	82823869	chr8	97238613	97238614	TRA	NA	-	+	[Svaba_SR=36,Svaba_PE=34],[Manta_PE=14,Manta_SR=30],[Lumpy_PE=6,Lumpy_SR=22]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=SEC31A;DisruptR=;ClosestL=;ClosestR=AP003115.1	89026738	97238582	20,82823867,97238614	0,0,0
chr4	82823983	82823984	chr8	96324292	96324293	TRA	NA	+	-	[Svaba_SR=33,Svaba_PE=0],[Manta_PE=14,Manta_SR=30],[Lumpy_PE=5,Lumpy_SR=16]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=SEC31A;DisruptR=PTDSS1;ClosestL=;ClosestR=RF00019	89026738	96324266	21,82823985,96324286	0,0,0
chr4	91384071	91384072	chr18	61626507	61626508	TRA	NA	+	-	[Svaba_SR=41,Svaba_PE=51],[Manta_PE=47,Manta_SR=34],[Lumpy_PE=39,Lumpy_SR=22]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=CCSER1;DisruptR=AC105094.2;ClosestL=;ClosestR=AC090409.1	91384038	61626460	30,91384073,61626506	0,0,0
chr4	91964436	91964437	chr4	91968879	91968880	INV	NA	-	-	[Svaba_SR=41,Svaba_PE=37],[Manta_PE=37,Manta_SR=37],[Lumpy_PE=22,Lumpy_SR=27]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;ClosestL=;ClosestR=	91964420	91964420	25,91964435,91968879	0,0,0
chr4	92714812	92714813	chr4	92741756	92741757	INV	NA	+	+	[Manta_PE=6,Manta_SR=7],[Lumpy_PE=5,Lumpy_SR=8]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=GRID2;DisruptR=GRID2;ClosestL=MTND1P19;ClosestR=	91964420	91964420	7,92714814,92741757	0,0,0
chr4	92714815	92714816	chr4	92741711	92741712	INV	NA	-	-	[Manta_PE=3,Manta_SR=4],[Lumpy_PE=5,Lumpy_SR=8]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=GRID2;DisruptR=GRID2;ClosestL=MTND1P19;ClosestR=	91964420	91964420	3,92714815,92741705	0,0,0
chr4	104438018	104438019	chr4	189036389	189036390	INV	NA	-	-	[Manta_PE=7,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=IL2|Tier1,FBXW7|Tier1,CASP3|Tier2,TET2|Tier1,LEF1|Tier1,FAT4|Tier1,FAT1|Tier1;DisruptL=;DisruptR=;ClosestL=;ClosestR=	91964420	190066290	3,104438194,189036344	0,0,0
chr4	168286143	168286144	chr20	14619539	14619540	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=13],[Lumpy_PE=4,Lumpy_SR=1]	lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=DDX60;DisruptR=MACROD2-IT1,MACROD2;ClosestL=;ClosestR=	190066290	8764420	0,0,0	0,0,0
chr4	189021274	189021275	chr4	189022112	189022113	DUP	NA	-	+	[Svaba_SR=19,Svaba_PE=28],[Manta_PE=23,Manta_SR=15],[Lumpy_PE=23,Lumpy_SR=12]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC122138.1;ClosestR=	190066290	190066290	14,189021273,189022113	0,0,0
chr4	189022112	189022113	chr4	189024736	189024737	DEL	NA	+	-	[Svaba_SR=39,Svaba_PE=0],[Manta_PE=18,Manta_SR=16],[Lumpy_PE=11,Lumpy_SR=12]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;ClosestL=;ClosestR=	190066290	190066290	0,0,0	0,0,0
chr5	6322108	6322109	chr5	6322738	6322739	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=10]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC02145;DisruptR=LINC02145;ClosestL=;ClosestR=	11484	11484	0,0,0	0,0,0
chr5	7300306	7300307	chr5	7300810	7300811	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=16]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC091951.1;DisruptR=AC091951.1;ClosestL=AC091951.2;ClosestR=AC091951.2	12810903	12810903	2,7300170,7300591	0,0,0
chr5	11509436	11509437	chr10	3336263	3336264	TRA	NA	+	-	[Svaba_SR=14,Svaba_PE=14],[Manta_PE=13,Manta_SR=10],[Lumpy_PE=10,Lumpy_SR=10]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=CTNND2|Tier2;DisruptL=CTNND2;DisruptR=;ClosestL=;ClosestR=	12810903	3411101	6,11509433,3336263	0,0,0
chr5	23767939	23767940	chr5	23769678	23769679	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=24],[Manta_PE=21,Manta_SR=15],[Lumpy_PE=18,Lumpy_SR=11]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	32366972	32366972	13,23767941,23769674	0,0,0
chr5	28710819	28710820	chr5	28711436	28711437	DEL	NA	+	-	[Svaba_SR=131,Svaba_PE=101],[Manta_PE=57,Manta_SR=86],[Lumpy_PE=57,Lumpy_SR=42]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	32366972	32366972	0,0,0	0,0,0
chr5	30463531	30463532	chr5	30475422	30475423	DEL	NA	+	-	[Svaba_SR=12,Svaba_PE=19],[Manta_PE=16,Manta_SR=13],[Lumpy_PE=14,Lumpy_SR=8]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;ClosestL=;ClosestR=	32366972	32366972	10,30463532,30475422	0,0,0
chr5	32366999	32367000	chr10	63904597	63904598	TRA	NA	+	+	[Svaba_SR=31,Svaba_PE=37],[Manta_PE=41,Manta_SR=25],[Lumpy_PE=31,Lumpy_SR=16]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ZFR;DisruptR=AC022387.1;Fusion=AC022387.1-ZFR;ClosestL=;ClosestR=RPL7AP50	32366973	63904755	16,32367001,63904598	0,0,0
chr5	43171736	43171737	chr5	43188686	43188687	DEL	NA	+	-	[Svaba_SR=14,Svaba_PE=21],[Manta_PE=16,Manta_SR=8],[Lumpy_PE=12,Lumpy_SR=4]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ZNF131;DisruptR=ZNF131;ClosestL=;ClosestR=NIM1K	32366973	32366973	8,43171736,43188686	0,0,0
chr5	49836878	49836879	chr19	17085941	17085942	TRA	NA	+	+	[Svaba_SR=11,Svaba_PE=6]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=MYO9B;ClosestL=;ClosestR=AC020908.3	32366973	15684659	7,49836879,17085942	0,0,0
chr5	55999435	55999436	chr5	56134518	56134519	DEL	NA	+	-	[Manta_PE=0,Manta_SR=23]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC016596.1,AC008892.1;DisruptR=ANKRD55;ClosestL=RF01210;ClosestR=RPL17P22	32366973	32366973	0,0,0	0,0,0
chr5	59193924	59193925	chr10	61749857	61749858	TRA	NA	+	+	[Manta_PE=0,Manta_SR=7]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PDE4D;DisruptR=CABCOCO1;Fusion=CABCOCO1-PDE4D;ClosestL=;ClosestR=	32366973	63904755	5,59193926,61749858	0,0,0
chr5	59747085	59747086	chr5	59755805	59755806	DUP	NA	-	+	[Manta_PE=3,Manta_SR=5],[Lumpy_PE=2,Lumpy_SR=3]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PDE4D;DisruptR=PDE4D;ClosestL=;ClosestR=	32366973	32366973	4,59747085,59755806	0,0,0
chr5	76588049	76588050	chr10	12934286	12934287	TRA	NA	-	+	[Svaba_SR=23,Svaba_PE=10],[Manta_PE=10,Manta_SR=17],[Lumpy_PE=9,Lumpy_SR=8]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=IQGAP2;DisruptR=CCDC3;ClosestL=AC026725.1;ClosestR=RNA5SP300	32366973	3411102	15,76588048,12934287	0,0,0
chr5	76588341	76588342	chr7	43643802	43643803	TRA	NA	+	+	[Svaba_SR=25,Svaba_PE=9],[Manta_PE=9,Manta_SR=18],[Lumpy_PE=5,Lumpy_SR=16]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=IQGAP2;DisruptR=COA1;Fusion=IQGAP2-COA1;ClosestL=AC026725.1;ClosestR=STK17A	32366973	43477639	16,76588334,43643803	0,0,0
chr5	78710196	78710197	chr5	78727227	78727228	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=24],[Manta_PE=20,Manta_SR=19],[Lumpy_PE=17,Lumpy_SR=1]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC008802.1,LHFPL2;DisruptR=LHFPL2;Fusion=LHFPL2+AC008802.1;ClosestL=;ClosestR=AC008802.1	32366973	32366973	14,78710197,78727227	0,0,0
chr5	101330082	101330083	chr5	101342606	101342607	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=23],[Manta_PE=18,Manta_SR=14],[Lumpy_PE=14,Lumpy_SR=11]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	164930824	164930824	11,101330082,101342606	0,0,0
chr5	102801795	102801796	chr5	102874958	102874959	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=15],[Manta_PE=15,Manta_SR=15]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PAM;DisruptR=PAM;ClosestL=;ClosestR=	164930824	164930824	0,0,0	0,0,0
chr5	107980664	107980665	chr13	43247827	43247828	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FBXL17;DisruptR=ENOX1;Fusion=ENOX1-FBXL17;ClosestL=;ClosestR=	164930824	28880402	3,107980645,43247829	0,0,0
chr5	114587648	114587649	chr5	114630660	114630661	DEL	NA	+	-	[Svaba_SR=16,Svaba_PE=22],[Manta_PE=16,Manta_SR=13],[Lumpy_PE=15,Lumpy_SR=10]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC010230.1;DisruptR=AC010230.1;ClosestL=LINC01957;ClosestR=	164930824	164930824	11,114587649,114630650	0,0,0
chr5	114622908	114622909	chr5	114630139	114630140	DEL	NA	+	-	[Svaba_SR=6,Svaba_PE=5]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC010230.1;DisruptR=AC010230.1;ClosestL=;ClosestR=	164930824	164930824	0,0,0	0,0,0
chr5	120820946	120820947	chr5	120829459	120829460	INV	NA	-	-	[Manta_PE=3,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	164930824	164930824	0,0,0	0,0,0
chr5	120820992	120820993	chr5	120828971	120828972	INV	NA	+	+	[Manta_PE=4,Manta_SR=3],[Lumpy_PE=3,Lumpy_SR=2]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	164930824	164930824	3,120820994,120828977	0,0,0
chr5	139904402	139904403	chr21	41878046	41878047	TRA	NA	+	+	[Svaba_SR=51,Svaba_PE=23],[Manta_PE=15,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=NRG2;DisruptR=PRDM15;ClosestL=;ClosestR=AP001619.1	164930824	41825926	0,0,0	0,0,0
chr5	139904402	139904403	chr7	82672674	82672675	TRA	NA	+	+	[Svaba_SR=37,Svaba_PE=17],[Manta_PE=15,Manta_SR=33],[Lumpy_PE=10,Lumpy_SR=27]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=NRG2;DisruptR=;ClosestL=;ClosestR=AC004006.1	164930824	84167674	24,139904402,82672675	0,0,0
chr5	154695628	154695629	chr5	154762331	154762332	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=31],[Manta_PE=28,Manta_SR=23],[Lumpy_PE=16,Lumpy_SR=14]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=LARP1;ClosestL=MIR1303;ClosestR=	164930824	164930824	19,154695630,154762324	0,0,0
chr5	164930879	164930880	chr10	29373648	29373649	TRA	NA	-	+	[Svaba_SR=29,Svaba_PE=8],[Manta_PE=5,Manta_SR=29]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC109466.1;DisruptR=;ClosestL=RNU6-209P;ClosestR=	164930825	29240716	12,164930880,29373649	0,0,0
chr5	166229022	166229023	chr5	176905028	176905029	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=10]	svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=NPM1|Tier1,TLX3|Tier1;DisruptL=;DisruptR=UIMC1;ClosestL=;ClosestR=HK3	164930825	180949083	0,0,0	0,0,0
chr5	166229023	166229024	chr5	171130631	171130632	DUP	NA	-	+	[Svaba_SR=24,Svaba_PE=4]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=RANBP17;ClosestL=;ClosestR=	164930825	164930825	0,0,0	0,0,0
chr5	166229096	166229097	chr13	103143785	103143786	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=11],[Manta_PE=9,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=14]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	164930825	107326494	0,0,0	0,0,0
chr5	169123666	169123667	chr5	171131427	171131428	DUP	NA	-	+	[Svaba_SR=23,Svaba_PE=22],[Manta_PE=18,Manta_SR=21],[Lumpy_PE=12,Lumpy_SR=15]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SLIT3;DisruptR=RANBP17;ClosestL=;ClosestR=	164930825	164930825	19,169123666,171131428	0,0,0
chr5	170686418	170686419	chr13	104720019	104720020	TRA	NA	-	-	[Svaba_SR=13,Svaba_PE=8],[Manta_PE=12,Manta_SR=16],[Lumpy_PE=10,Lumpy_SR=1]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=KCNIP1;DisruptR=;ClosestL=AC027312.1;ClosestR=	164930825	107326494	0,0,0	0,0,0
chr5	170686434	170686435	chr13	104711356	104711357	TRA	NA	+	+	[Svaba_SR=23,Svaba_PE=14],[Manta_PE=17,Manta_SR=21]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=KCNIP1;DisruptR=;ClosestL=AC027312.1;ClosestR=	164930825	107326494	0,0,0	0,0,0
chr5	171130474	171130475	chr5	176905028	176905029	DUP	NA	-	+	[Svaba_SR=12,Svaba_PE=7],[Manta_PE=7,Manta_SR=9],[Lumpy_PE=7,Lumpy_SR=1]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=NPM1|Tier1,TLX3|Tier1;DisruptL=RANBP17;DisruptR=UIMC1;ClosestL=;ClosestR=HK3	164930825	180949083	0,0,0	0,0,0
chr5	171130631	171130632	chr13	103143872	103143873	TRA	NA	+	+	[Svaba_SR=36,Svaba_PE=5]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RANBP17;DisruptR=;ClosestL=;ClosestR=	164930825	107326494	0,0,0	0,0,0
chr5	172804771	172804772	chr13	104711184	104711185	TRA	NA	-	-	[Manta_PE=6,Manta_SR=10],[Lumpy_PE=3,Lumpy_SR=9]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC110011.1;ClosestR=	164930825	107326494	11,172804773,104711181	0,0,0
chr5	173535074	173535075	chr21	17229345	17229346	TRA	NA	+	-	[Svaba_SR=13,Svaba_PE=15],[Manta_PE=11,Manta_SR=12],[Lumpy_PE=7,Lumpy_SR=10]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=NEK4P1	180949083	17474345	11,173535079,17229342	0,0,0
chr5	179626987	179626988	chr5	179641488	179641489	INV	NA	+	+	[Svaba_SR=84,Svaba_PE=86],[Manta_PE=87,Manta_SR=71],[Lumpy_PE=79,Lumpy_SR=29]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=HNRNPH1;DisruptR=;ClosestL=RF00017;ClosestR=C5orf60	180949083	180949083	45,179626986,179641489	0,0,0
chr6	5651670	5651671	chr7	137445350	137445351	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=9],[Manta_PE=6,Manta_SR=16],[Lumpy_PE=5,Lumpy_SR=15]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FARS2;DisruptR=DGKI;Fusion=DGKI-FARS2;ClosestL=AL022097.1;ClosestR=	882088	137445254	10,5651672,137445274	0,0,0
chr6	5651755	5651756	chr10	37195842	37195843	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=16],[Manta_PE=7,Manta_SR=11],[Lumpy_PE=5,Lumpy_SR=7]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FARS2;DisruptR=ANKRD30A;Fusion=FARS2-ANKRD30A;ClosestL=AL022097.1;ClosestR=	882088	37167258	7,5651754,37195765	0,0,0
chr6	10615715	10615716	chr6	10671380	10671381	INV	NA	-	-	[Manta_PE=7,Manta_SR=7],[Lumpy_PE=3,Lumpy_SR=6]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=GCNT2;DisruptR=;ClosestL=GCNT2P;ClosestR=C6orf52	882088	882088	7,10615718,10671378	0,0,0
chr6	24909910	24909911	chr13	23788151	23788152	TRA	NA	+	-	[Svaba_SR=26,Svaba_PE=29],[Manta_PE=29,Manta_SR=25],[Lumpy_PE=26,Lumpy_SR=13]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=RIPOR2;DisruptR=MIPEP;Fusion=MIPEP-RIPOR2;ClosestL=;ClosestR=	24909816	23788057	2,24909916,23788151	0,0,0
chr6	31282776	31282777	chr6	31676535	31676536	DUP	NA	-	+	[Svaba_SR=45,Svaba_PE=48],[Manta_PE=44,Manta_SR=38],[Lumpy_PE=36,Lumpy_SR=7]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=HLA-B;DisruptR=;ClosestL=RPL3P2;ClosestR=LY6G5C	32487100	32487100	30,31282778,31676536	0,0,0
chr6	36092690	36092691	chr11	72659713	72659714	TRA	NA	+	-	[Svaba_SR=31,Svaba_PE=29],[Manta_PE=24,Manta_SR=28],[Lumpy_PE=11,Lumpy_SR=26]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MAPK14;DisruptR=PDE2A;ClosestL=Z95152.1;ClosestR=AP003065.1	36092606	72659618	22,36092689,72659713	0,0,0
chr6	37947053	37947054	chr6	37948416	37948417	INV	NA	-	-	[Svaba_SR=32,Svaba_PE=40],[Manta_PE=41,Manta_SR=34],[Lumpy_PE=32,Lumpy_SR=22]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ZFAND3;DisruptR=ZFAND3;ClosestL=;ClosestR=	37947068	37947069	0,0,0	0,0,0
chr6	38119595	38119596	chr11	45539585	45539586	TRA	NA	-	-	[Svaba_SR=36,Svaba_PE=42],[Manta_PE=45,Manta_SR=26],[Lumpy_PE=30,Lumpy_SR=22]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ZFAND3;DisruptR=AC103855.2;Fusion=AC103855.2-ZFAND3;ClosestL=;ClosestR=	38141254	45539525	21,38119596,45539585	0,0,0
chr6	38131029	38131030	chr6	38141273	38141274	INV	NA	+	+	[Svaba_SR=52,Svaba_PE=40],[Manta_PE=36,Manta_SR=45],[Lumpy_PE=32,Lumpy_SR=27]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ZFAND3;DisruptR=ZFAND3;ClosestL=;ClosestR=	38141254	38141255	2,38131032,38141271	0,0,0
chr6	38475453	38475454	chr6	38488043	38488044	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=19],[Manta_PE=16,Manta_SR=15],[Lumpy_PE=12,Lumpy_SR=13]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=BTBD9;DisruptR=BTBD9;ClosestL=BTBD9-AS1;ClosestR=BTBD9-AS1	38141255	38141255	14,38475453,38488043	0,0,0
chr6	51934058	51934059	chr6	51937863	51937864	INV	NA	+	+	[Svaba_SR=16,Svaba_PE=26],[Manta_PE=28,Manta_SR=13],[Lumpy_PE=26,Lumpy_SR=8]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PKHD1;DisruptR=PKHD1;ClosestL=;ClosestR=	52221178	52221178	12,51934060,51937864	0,0,0
chr6	52220975	52220976	chr13	110468790	110468791	TRA	NA	-	+	[Svaba_SR=27,Svaba_PE=30],[Manta_PE=28,Manta_SR=23],[Lumpy_PE=17,Lumpy_SR=18]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=COL4A2;ClosestL=IL17F;ClosestR=COL4A2-AS2	52221178	110418576	21,52220974,110468791	0,0,0
chr6	52542328	52542329	chr14	102959581	102959582	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TRAM2;DisruptR=CDC42BPB;Fusion=TRAM2-CDC42BPB;ClosestL=EFHC1;ClosestR=	52679253	104243063	0,0,0	0,0,0
chr6	52679254	52679255	chr18	23971471	23971472	TRA	NA	+	+	[Svaba_SR=59,Svaba_PE=61],[Manta_PE=70,Manta_SR=51],[Lumpy_PE=47,Lumpy_SR=24]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TMEM14A;DisruptR=AC010754.1;Fusion=TMEM14A-AC010754.1;ClosestL=GSTA8P;ClosestR=LAMA3	52679254	23971375	42,52679253,23971472	0,0,0
chr6	53892609	53892610	chr6	53893327	53893328	DEL	NA	+	-	[Manta_PE=24,Manta_SR=25],[Lumpy_PE=20,Lumpy_SR=19]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LRRC1;DisruptR=LRRC1;ClosestL=;ClosestR=	54303155	54303155	22,53892611,53893328	0,0,0
chr6	54303391	54303392	chr15	76561854	76561855	TRA	NA	+	-	[Svaba_SR=19,Svaba_PE=0],[Manta_PE=7,Manta_SR=21],[Lumpy_PE=4,Lumpy_SR=17]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=SCAPER;ClosestL=TINAG;ClosestR=	54303156	72362590	16,54303392,76561854	0,0,0
chr6	54303442	54303443	chr16	67652158	67652159	TRA	NA	+	+	[Manta_PE=10,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CARMIL2;ClosestL=TINAG;ClosestR=ACD	54303156	90226217	0,0,0	0,0,0
chr6	58157667	58157668	chr13	110418585	110418586	TRA	NA	-	+	[Svaba_SR=54,Svaba_PE=74],[Manta_PE=26,Manta_SR=45],[Lumpy_PE=20,Lumpy_SR=7]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AL445250.1;DisruptR=COL4A2;Fusion=COL4A2-AL445250.1;ClosestL=;ClosestR=AL159153.1	59823890	110418576	39,58157667,110418586	0,0,0
chr6	58190428	58190429	chr11	78640457	78640458	TRA	NA	+	+	[Svaba_SR=50,Svaba_PE=50],[Manta_PE=49,Manta_SR=32]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AL445250.1;DisruptR=;ClosestL=;ClosestR=TENM4	59823890	78640370	28,58190430,78640458	0,0,0
chr6	73497654	73497655	chr20	5744486	5744487	TRA	NA	+	-	[Manta_PE=8,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MTO1;DisruptR=;ClosestL=AL603910.1;ClosestR=SHLD1	78257462	8764419	0,0,0	0,0,0
chr6	82898488	82898489	chr6	82899849	82899850	DEL	NA	+	-	[Svaba_SR=14,Svaba_PE=17],[Manta_PE=16,Manta_SR=14],[Lumpy_PE=14,Lumpy_SR=7]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=UBE3D;DisruptR=UBE3D;ClosestL=;ClosestR=	78326602	78326602	10,82898490,82899849	0,0,0
chr6	85371209	85371210	chr11	69182921	69182922	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=20],[Manta_PE=7,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=LINC02535;ClosestR=AP003071.2	78326602	69098162	0,0,0	0,0,0
chr6	108428792	108428793	chr6	108701375	108701376	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=25],[Manta_PE=21,Manta_SR=15],[Lumpy_PE=15,Lumpy_SR=12]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=FOXO3|Tier1;DisruptL=AFG1L;DisruptR=;ClosestL=;ClosestR=FOXO3	129707604	129707604	12,108428791,108701375	0,0,0
chr6	119711508	119711509	chr6	119739228	119739229	DUP	NA	-	+	[Lumpy_PE=3,Lumpy_SR=2]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	129707604	129707604	2,119711512,119739228	0,0,0
chr6	129707662	129707663	chr6	130004047	130004048	DUP	NA	-	+	[Svaba_SR=50,Svaba_PE=72],[Manta_PE=69,Manta_SR=40],[Lumpy_PE=59,Lumpy_SR=29]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ARHGAP18;DisruptR=;ClosestL=;ClosestR=L3MBTL3	129707605	130003967	33,129707665,130004048	0,0,0
chr6	144660334	144660335	chr21	32343657	32343658	TRA	NA	+	+	[Manta_PE=2,Manta_SR=19],[Lumpy_PE=2,Lumpy_SR=12]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=UTRN;DisruptR=URB1;Fusion=UTRN-URB1;ClosestL=;ClosestR=	130003967	32739659	10,144660336,32343658	0,0,0
chr6	166891543	166891544	chr16	13287330	13287331	TRA	NA	-	-	[Svaba_SR=21,Svaba_PE=28],[Manta_PE=27,Manta_SR=15],[Lumpy_PE=21,Lumpy_SR=13]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AL159163.1,RPS6KA2;DisruptR=U91319.1;Fusion=AL159163.1-U91319.1|RPS6KA2-U91319.1;ClosestL=RPS6KA2-AS1;ClosestR=	166891771	13284478	14,166891543,13287330	0,0,0
chr6	168164289	168164290	chr6	168191518	168191519	DUP	NA	-	+	[Svaba_SR=33,Svaba_PE=17],[Manta_PE=18,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=AL611929.1	166891772	166891772	0,0,0	0,0,0
chr7	29985175	29985176	chr11	76901510	76901511	TRA	NA	-	+	[Svaba_SR=50,Svaba_PE=3]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SCRN1;DisruptR=ACER3;ClosestL=AC007285.1;ClosestR=	43477638	78640369	0,0,0	0,0,0
chr7	29985175	29985176	chr22	28499903	28499904	TRA	NA	-	+	[Svaba_SR=32,Svaba_PE=0],[Manta_PE=8,Manta_SR=28],[Lumpy_PE=2,Lumpy_SR=15]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SCRN1;DisruptR=TTC28;Fusion=SCRN1-TTC28;ClosestL=AC007285.1;ClosestR=	43477638	29344638	19,29985176,28499904	0,0,0
chr7	29985277	29985278	chr21	14331478	14331479	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=12],[Manta_PE=10,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SCRN1;DisruptR=ABCC13;ClosestL=AC007285.1;ClosestR=	43477638	13507201	0,0,0	0,0,0
chr7	43477683	43477684	chr17	67148382	67148383	TRA	NA	-	+	[Svaba_SR=66,Svaba_PE=86],[Manta_PE=76,Manta_SR=60],[Lumpy_PE=59,Lumpy_SR=40]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=HECW1;DisruptR=HELZ;ClosestL=;ClosestR=	43477639	67102560	43,43477682,67148383	0,0,0
chr7	44883007	44883008	chr7	44913973	44913974	DUP	NA	-	+	[Svaba_SR=70,Svaba_PE=59],[Manta_PE=71,Manta_SR=63],[Lumpy_PE=62,Lumpy_SR=39]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PURB;DisruptR=;ClosestL=MIR4657;ClosestR=AC004854.1	43477639	43477639	46,44883003,44913975	0,0,0
chr7	47787889	47787890	chr21	13481495	13481496	TRA	NA	-	+	[Svaba_SR=21,Svaba_PE=14],[Manta_PE=8,Manta_SR=13]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=HUS1,PKD1L1;DisruptR=GTF2IP2;Fusion=HUS1-GTF2IP2|PKD1L1-GTF2IP2;ClosestL=C7orf69;ClosestR=VN1R8P	43477639	13507200	13,47787891,13481496	0,0,0
chr7	47788066	47788067	chr7	57377873	57377874	DEL	NA	+	-	[Svaba_SR=19,Svaba_PE=17],[Manta_PE=11,Manta_SR=19],[Lumpy_PE=7,Lumpy_SR=12]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=ZNF479|Tier2,EGFR|Tier1,IKZF1|Tier1;DisruptL=HUS1,PKD1L1;DisruptR=;ClosestL=C7orf69;ClosestR=	43477639	57487363	15,47788066,57377873	0,0,0
chr7	53748552	53748553	chr7	53753362	53753363	DEL	NA	+	-	[Svaba_SR=65,Svaba_PE=79],[Manta_PE=74,Manta_SR=54],[Lumpy_PE=48,Lumpy_SR=43]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC01446;DisruptR=LINC01446;ClosestL=;ClosestR=	57487363	57487363	39,53748553,53753362	0,0,0
chr7	57224566	57224567	chr7	63487943	63487944	INV	NA	-	-	[Svaba_SR=18,Svaba_PE=12]	svaba	HCC-1143_80--HCC-1143BL_40	known=;gap;DisruptL=;DisruptR=;ClosestL=AC099654.1;ClosestR=AC006457.1	57487363	62742772	12,57224563,63487940	0,0,0
chr7	57907930	57907931	chr7	57908528	57908529	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	57497083	57497083	0,0,0	0,0,0
chr7	61041203	61041204	chr18	21481532	21481533	TRA	NA	-	-	[Lumpy_PE=3,Lumpy_SR=1]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=GREB1L;ClosestL=;ClosestR=	62116180	20553042	3,61041202,21481531	0,0,0
chr7	62742736	62742737	chr7	87327162	87327163	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=8],[Manta_PE=8,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=SBDS|Tier1,ELN|Tier2,HIP1|Tier1,GRM3|Tier2;DisruptL=;DisruptR=TP53TG1;ClosestL=;ClosestR=RF02195	62742771	84789193	0,0,0	0,0,0
chr7	62742736	62742737	chr8	134414517	134414518	TRA	NA	+	+	[Svaba_SR=12,Svaba_PE=5],[Manta_PE=6,Manta_SR=10]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	62742771	145078494	9,62742738,134414518	0,0,0
chr7	69920183	69920184	chr7	70236713	70236714	DEL	NA	+	-	[Svaba_SR=12,Svaba_PE=18],[Manta_PE=17,Manta_SR=11],[Lumpy_PE=11,Lumpy_SR=10]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AUTS2;DisruptR=AUTS2;ClosestL=;ClosestR=	69920124	70236680	8,69920183,70236713	0,0,0
chr7	82613835	82613836	chr21	41878419	41878420	TRA	NA	-	-	[Svaba_SR=12,Svaba_PE=7],[Manta_PE=7,Manta_SR=10],[Lumpy_PE=4,Lumpy_SR=6]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=PRDM15;ClosestL=;ClosestR=AP001619.1	84167674	41825926	8,82613834,41878418	0,0,0
chr7	82616051	82616052	chr10	51349321	51349322	TRA	NA	+	-	[Svaba_SR=34,Svaba_PE=8],[Manta_PE=6,Manta_SR=29],[Lumpy_PE=4,Lumpy_SR=27]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=PRKG1;ClosestL=;ClosestR=	84167674	39580117	23,82616053,51349321	0,0,0
chr7	82616052	82616053	chr17	20111623	20111624	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=9],[Manta_PE=8,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=SPECC1|Tier2;DisruptL=;DisruptR=SPECC1;ClosestL=;ClosestR=KCTD9P1	84167674	21658447	0,0,0	0,0,0
chr7	82672505	82672506	chr21	41878046	41878047	TRA	NA	-	+	[Svaba_SR=26,Svaba_PE=28],[Manta_PE=18,Manta_SR=21],[Lumpy_PE=13,Lumpy_SR=11]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=PRDM15;ClosestL=AC004006.1;ClosestR=AP001619.1	84167674	41825926	14,82672505,41878047	0,0,0
chr7	86257760	86257761	chr21	26634844	26634845	TRA	NA	-	+	[Svaba_SR=23,Svaba_PE=23],[Manta_PE=20,Manta_SR=20],[Lumpy_PE=15,Lumpy_SR=14]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	84789193	26635290	20,86257759,26634845	0,0,0
chr7	87327163	87327164	chr8	134414383	134414384	TRA	NA	-	-	[Svaba_SR=18,Svaba_PE=0],[Manta_PE=0,Manta_SR=17]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TP53TG1;DisruptR=;ClosestL=RF02195;ClosestR=	84789193	145078494	15,87327163,134414383	0,0,0
chr7	89265302	89265303	chr7	89268691	89268692	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=16],[Manta_PE=17,Manta_SR=16],[Lumpy_PE=14,Lumpy_SR=1]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ZNF804B;DisruptR=ZNF804B;ClosestL=;ClosestR=	92202778	92202778	0,0,0	0,0,0
chr7	92202777	92202778	chr7	92380664	92380665	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=24],[Manta_PE=15,Manta_SR=23],[Lumpy_PE=11,Lumpy_SR=16]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC000120.1,KRIT1;DisruptR=ANKIB1;ClosestL=RF00019;ClosestR=	92202778	92380732	18,92202778,92380664	0,0,0
chr7	116918744	116918745	chrX	57506628	57506629	TRA	NA	-	+	[Svaba_SR=21,Svaba_PE=21],[Manta_PE=15,Manta_SR=16]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CAPZA2;DisruptR=;ClosestL=RF00019;ClosestR=FAAH2	116918673	57361937	13,116918745,57506629	0,0,0
chr7	137445279	137445280	chr10	37195765	37195766	TRA	NA	-	-	[Svaba_SR=32,Svaba_PE=15],[Manta_PE=8,Manta_SR=13]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=DGKI;DisruptR=ANKRD30A;Fusion=DGKI-ANKRD30A;ClosestL=;ClosestR=	137445254	37167258	0,0,0	0,0,0
chr7	140911265	140911266	chr7	140955783	140955784	INV	NA	-	-	[Svaba_SR=22,Svaba_PE=22],[Manta_PE=19,Manta_SR=19],[Lumpy_PE=12,Lumpy_SR=14]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=BRAF|Tier1;DisruptL=BRAF;DisruptR=;ClosestL=;ClosestR=	137445254	137445254	17,140911266,140955783	0,0,0
chr7	141230709	141230710	chr7	141238330	141238331	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=29],[Manta_PE=23,Manta_SR=17],[Lumpy_PE=17,Lumpy_SR=12]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TMEM178B;DisruptR=TMEM178B;ClosestL=;ClosestR=	144556595	144556595	15,141230711,141238330	0,0,0
chr7	141234566	141234567	chr7	141311291	141311292	INV	NA	+	+	[Svaba_SR=24,Svaba_PE=26],[Manta_PE=16,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=13]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TMEM178B;DisruptR=TMEM178B;ClosestL=;ClosestR=	144556595	144556595	6,141234568,141311292	0,0,0
chr7	150360465	150360466	chr20	22471887	22471888	TRA	NA	+	-	[Manta_PE=9,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC005586.1;ClosestR=AL133464.1	144556596	21885645	0,0,0	0,0,0
chr8	10846875	10846876	chr20	47268863	47268864	TRA	NA	-	-	[Svaba_SR=18,Svaba_PE=0],[Manta_PE=13,Manta_SR=21],[Lumpy_PE=7,Lumpy_SR=15]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=ZMYND8;ClosestL=AC011008.1;ClosestR=	71162	39349551	20,10846878,47268863	0,0,0
chr8	10847021	10847022	chr20	47225235	47225236	TRA	NA	+	+	[Svaba_SR=26,Svaba_PE=21],[Manta_PE=19,Manta_SR=21],[Lumpy_PE=7,Lumpy_SR=14]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=ZMYND8;ClosestL=AC011008.1;ClosestR=	71162	39349551	17,10847023,47225236	0,0,0
chr8	13703718	13703719	chr19	21583808	21583809	TRA	NA	-	-	[Manta_PE=4,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC022880.2;DisruptR=AC123912.4;Fusion=AC123912.4-AC022880.2;ClosestL=;ClosestR=AC123912.2	71162	20490395	0,0,0	0,0,0
chr8	13704170	13704171	chr19	21583861	21583862	TRA	NA	+	+	[Manta_PE=4,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC022880.2;DisruptR=AC123912.4;Fusion=AC022880.2-AC123912.4;ClosestL=;ClosestR=AC123912.2	71162	20490395	0,0,0	0,0,0
chr8	38073703	38073704	chr8	38074256	38074257	DEL	NA	+	-	[Svaba_SR=43,Svaba_PE=57],[Manta_PE=44,Manta_SR=33],[Lumpy_PE=32,Lumpy_SR=14]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AP006545.1;ClosestR=AP006545.1	36461421	36461421	20,38073700,38074256	0,0,0
chr8	43475992	43475993	chr11	70550642	70550643	TRA	NA	-	+	[Svaba_SR=201,Svaba_PE=240],[Manta_PE=202,Manta_SR=192],[Lumpy_PE=138,Lumpy_SR=143]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=SHANK2;ClosestL=AC134698.4;ClosestR=	43475933	70550614	90,43475994,70550643	0,0,0
chr8	43546482	43546483	chr8	43547124	43547125	DEL	NA	+	-	[Svaba_SR=4,Svaba_PE=0]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC134698.2;ClosestR=AC134698.2	43475933	43475933	2,43546458,43547124	0,0,0
chr8	43561809	43561810	chr8	43562355	43562356	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=13]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC134698.2;ClosestR=AC134698.2	43646293	43646293	0,0,0	0,0,0
chr8	43634263	43634264	chr8	43635536	43635537	INV	NA	+	+	[Manta_PE=51,Manta_SR=62],[Lumpy_PE=41,Lumpy_SR=15]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	43646293	43646293	26,43634275,43635537	0,0,0
chr8	43646325	43646326	chr14	104763654	104763655	TRA	NA	+	+	[Svaba_SR=133,Svaba_PE=136],[Manta_PE=126,Manta_SR=115],[Lumpy_PE=81,Lumpy_SR=81]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=SIVA1;ClosestL=;ClosestR=AL583722.2	43646294	104243064	65,43646326,104763655	0,0,0
chr8	46943846	46943847	chr8	60480162	60480163	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=22],[Manta_PE=15,Manta_SR=16]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=TCEA1|Tier1,PLAG1|Tier1,CHCHD7|Tier1;DisruptL=;DisruptR=LINC01301;ClosestL=AC091163.2;ClosestR=	45740171	60480054	16,46943847,60480162	0,0,0
chr8	47813737	47813738	chr11	58189360	58189361	TRA	NA	-	-	[Svaba_SR=42,Svaba_PE=43],[Manta_PE=40,Manta_SR=36],[Lumpy_PE=28,Lumpy_SR=24]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=PRKDC;DisruptR=OR9Q2;Fusion=PRKDC-OR9Q2;ClosestL=RF00019;ClosestR=OR9Q1	45740171	58828468	29,47813739,58189360	0,0,0
chr8	48173949	48173950	chr10	128059808	128059809	TRA	NA	-	-	[Manta_PE=7,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=PTPRE;ClosestL=AC104989.1;ClosestR=	45740171	133787316	0,0,0	0,0,0
chr8	60642425	60642426	chr8	60724569	60724570	DEL	NA	+	-	[Svaba_SR=33,Svaba_PE=29],[Manta_PE=24,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=11]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CHD7;ClosestL=AC068389.1;ClosestR=	60480054	60480054	16,60642425,60724569	0,0,0
chr8	80571008	80571009	chr16	22585150	22585151	TRA	NA	-	-	[Manta_PE=3,Manta_SR=15]	manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC009812.2;ClosestR=AC106788.1	69392452	13284478	12,80571008,22585149	0,0,0
chr8	86158943	86158944	chr8	86203823	86203824	INV	NA	+	+	[Svaba_SR=22,Svaba_PE=5]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=AC084128.1;ClosestL=ATP6V0D2;ClosestR=SLC7A13	96324265	96324265	6,86158943,86203824	0,0,0
chr8	86159415	86159416	chr8	86201237	86201238	DEL	NA	+	-	[Svaba_SR=23,Svaba_PE=31],[Manta_PE=22,Manta_SR=24],[Lumpy_PE=16,Lumpy_SR=19]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=AC084128.1;ClosestL=ATP6V0D2;ClosestR=SLC7A13	96324265	96324265	19,86159417,86201235	0,0,0
chr8	86201237	86201238	chr8	86204869	86204870	DUP	NA	-	+	[Svaba_SR=38,Svaba_PE=4]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC084128.1;DisruptR=AC084128.1;ClosestL=SLC7A13;ClosestR=SLC7A13	96324265	96324265	0,0,0	0,0,0
chr8	88879692	88879693	chr8	102821044	102821045	INV	NA	+	+	[Svaba_SR=19,Svaba_PE=0],[Manta_PE=4,Manta_SR=17]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=COX6C|Tier2,NBN|Tier1,CDH17|Tier2,PABPC1|Tier2,RUNX1T1|Tier1,UBR5|Tier1;DisruptL=;DisruptR=;ClosestL=;ClosestR=AZIN1	96324265	101450437	10,88879694,102821045	0,0,0
chr8	88879692	88879693	chr8	88884416	88884417	DEL	NA	+	-	[Svaba_SR=25,Svaba_PE=0],[Manta_PE=9,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	96324265	96324265	0,0,0	0,0,0
chr8	88884416	88884417	chr8	102820935	102820936	INV	NA	-	-	[Svaba_SR=15,Svaba_PE=6],[Manta_PE=6,Manta_SR=13]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=COX6C|Tier2,NBN|Tier1,CDH17|Tier2,PABPC1|Tier2,RUNX1T1|Tier1,UBR5|Tier1;DisruptL=;DisruptR=;ClosestL=;ClosestR=AZIN1	96324265	101450437	11,88884418,102820935	0,0,0
chr8	89211648	89211649	chr10	102843876	102843877	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=PFN1P11;ClosestL=;ClosestR=PTGES3P4	96324265	133787316	0,0,0	0,0,0
chr8	94880300	94880301	chr8	94902717	94902718	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=29],[Manta_PE=24,Manta_SR=15],[Lumpy_PE=20,Lumpy_SR=12]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=INTS8,CCNE2;DisruptR=NDUFAF6;Fusion=INTS8+NDUFAF6;ClosestL=AC087752.4;ClosestR=CCNE2	96324265	96324265	12,94880302,94902717	0,0,0
chr8	96324291	96324292	chr8	97238614	97238615	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=22],[Manta_PE=31,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PTDSS1;DisruptR=;ClosestL=RF00019;ClosestR=AP003115.1	96324266	97238582	0,0,0	0,0,0
chr8	101450517	101450518	chr11	69897840	69897841	TRA	NA	-	+	[Svaba_SR=36,Svaba_PE=41],[Manta_PE=40,Manta_SR=28],[Lumpy_PE=30,Lumpy_SR=23]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR=AP007216.1	101450437	69779347	23,101450517,69897841	0,0,0
chr8	101451844	101451845	chr11	69897285	69897286	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=30],[Manta_PE=26,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR=AP007216.1	101450437	69779347	0,0,0	0,0,0
chr8	101451845	101451846	chr8	113801324	113801325	INV	NA	-	-	[Svaba_SR=62,Svaba_PE=10],[Manta_PE=24,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=15]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=EIF3E|Tier1,UBR5|Tier1,RSPO2|Tier1,CSMD3|Tier2;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR=	101450437	113847102	5,101451839,113801145	0,0,0
chr8	102577650	102577651	chr8	102826797	102826798	DUP	NA	-	+	[Manta_PE=5,Manta_SR=4],[Lumpy_PE=3,Lumpy_SR=4]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=AZIN1;ClosestL=ODF1;ClosestR=GASAL1	101450437	101450437	4,102577656,102826804	0,0,0
chr8	112077674	112077675	chr8	112087837	112087838	DEL	NA	+	-	[Svaba_SR=16,Svaba_PE=22],[Manta_PE=21,Manta_SR=14],[Lumpy_PE=12,Lumpy_SR=9]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	113847102	113847102	13,112077673,112087837	0,0,0
chr8	113730713	113730714	chr8	113847230	113847231	INV	NA	+	+	[Svaba_SR=34,Svaba_PE=31],[Manta_PE=32,Manta_SR=27],[Lumpy_PE=29,Lumpy_SR=22]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	113847102	113847103	20,113730714,113847231	0,0,0
chr8	113801314	113801315	chr11	69780162	69780163	TRA	NA	+	+	[Svaba_SR=69,Svaba_PE=79],[Manta_PE=78,Manta_SR=58],[Lumpy_PE=51,Lumpy_SR=49]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=FGF4	113847102	69779347	45,113801316,69780163	0,0,0
chr8	113801461	113801462	chr11	69897286	69897287	TRA	NA	+	-	[Svaba_SR=54,Svaba_PE=42],[Manta_PE=39,Manta_SR=50],[Lumpy_PE=24,Lumpy_SR=39]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=AP007216.1	113847102	69779347	37,113801459,69897286	0,0,0
chr8	113817587	113817588	chr8	114411853	114411854	INV	NA	-	-	[Svaba_SR=52,Svaba_PE=42],[Manta_PE=45,Manta_SR=45],[Lumpy_PE=26,Lumpy_SR=31]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=	113847102	114412877	33,113817589,114411853	0,0,0
chr8	117297894	117297895	chr8	117323013	117323014	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=25],[Manta_PE=25,Manta_SR=18],[Lumpy_PE=17,Lumpy_SR=16]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=RF00322;ClosestR=RF00322	114412878	114412878	20,117297889,117323013	0,0,0
chr8	118959452	118959453	chr16	67651851	67651852	TRA	NA	-	-	[Svaba_SR=17,Svaba_PE=4],[Manta_PE=4,Manta_SR=14],[Lumpy_PE=2,Lumpy_SR=10]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CARMIL2;ClosestL=TNFRSF11B;ClosestR=ACD	121696690	90226217	14,118959451,67651851	0,0,0
chr8	118959598	118959599	chr9	131565190	131565191	TRA	NA	+	+	[Svaba_SR=24,Svaba_PE=8],[Manta_PE=8,Manta_SR=20],[Lumpy_PE=8,Lumpy_SR=12]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=TNFRSF11B;ClosestR=PRRT1B	121696690	138313848	16,118959600,131565191	0,0,0
chr8	122992392	122992393	chr8	123075947	123075948	DEL	NA	+	-	[Svaba_SR=59,Svaba_PE=64],[Manta_PE=52,Manta_SR=53],[Lumpy_PE=30,Lumpy_SR=41]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=TBC1D31;ClosestL=AC104316.2;ClosestR=	121696691	121696691	10,122992391,123075947	0,0,0
chr8	124474058	124474059	chr8	124482945	124482946	DEL	NA	+	-	[Manta_PE=12,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RNF139-AS1;DisruptR=RNF139;ClosestL=RNF139;ClosestR=TATDN1	121696691	121696691	0,0,0	0,0,0
chr8	140358492	140358493	chrX	56991208	56991209	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TRAPPC9;DisruptR=SPIN3;Fusion=SPIN3-TRAPPC9;ClosestL=;ClosestR=AL139397.1	145078494	56991084	2,140358494,56991091	0,0,0
chr8	143023980	143023981	chr8	143042570	143042571	DEL	NA	+	-	[Svaba_SR=40,Svaba_PE=41],[Manta_PE=38,Manta_SR=29],[Lumpy_PE=30,Lumpy_SR=23]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=C8orf31;ClosestL=LY6E;ClosestR=AK3P2	145078494	145078494	24,143023978,143042570	0,0,0
chr8	144267751	144267752	chr8	144315558	144315559	DEL	NA	+	-	[Svaba_SR=18,Svaba_PE=31],[Manta_PE=29,Manta_SR=17],[Lumpy_PE=21,Lumpy_SR=13]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SCX,BOP1;DisruptR=DGAT1;Fusion=DGAT1+BOP1;ClosestL=MIR7112;ClosestR=AC233992.1	145078494	145078494	14,144267746,144315558	0,0,0
chr9	42783552	42783553	chr9	64784638	64784639	INV	NA	-	-	[Manta_PE=3,Manta_SR=7]	manta	HCC-1143_80--HCC-1143BL_40	known=;gap;DisruptL=;DisruptR=;ClosestL=ADGRF5P2;ClosestR=IGKV1OR-2	45516998	66040021	6,42783556,64784635	0,0,0
chr9	72457967	72457968	chr17	1788610	1788611	TRA	NA	+	+	[Svaba_SR=20,Svaba_PE=4],[Manta_PE=4,Manta_SR=20],[Lumpy_PE=3,Lumpy_SR=9]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=SMYD4;ClosestL=AL445646.1;ClosestR=SERPINF1	66040022	168977	14,72457969,1788612	0,0,0
chr9	72457967	72457968	chr17	35740200	35740201	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=12],[Manta_PE=12,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=AL445646.1;ClosestR=GAS2L2	66040022	36041470	0,0,0	0,0,0
chr9	94312707	94312708	chr9	94313512	94313513	DEL	NA	+	-	[Manta_PE=6,Manta_SR=24]	manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;ClosestL=NUTM2F;ClosestR=NUTM2F	66040022	66040022	25,94312709,94313513	0,0,0
chr9	113363750	113363751	chr9	113614603	113614604	DUP	NA	-	+	[Svaba_SR=17,Svaba_PE=12],[Manta_PE=11,Manta_SR=16],[Lumpy_PE=10,Lumpy_SR=2]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=BSPRY;DisruptR=AL162727.3;ClosestL=HDHD3;ClosestR=AL162727.1	138313848	138313848	12,113363742,113614609	0,0,0
chr9	119084271	119084272	chr19	4778245	4778246	TRA	NA	-	+	[Manta_PE=4,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=MIR7-3HG	138313848	90733	0,0,0	0,0,0
chr9	119084714	119084715	chr19	4778382	4778383	TRA	NA	+	-	[Manta_PE=4,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=MIR7-3HG	138313848	90733	5,119084537,4778353	0,0,0
chr9	123290032	123290033	chr11	76901313	76901314	TRA	NA	+	-	[Svaba_SR=34,Svaba_PE=24],[Manta_PE=19,Manta_SR=28],[Lumpy_PE=10,Lumpy_SR=21]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=ACER3;ClosestL=;ClosestR=	138313848	78640369	22,123290034,76901313	0,0,0
chr9	123290032	123290033	chr22	28499617	28499618	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=10]	svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=TTC28;ClosestL=;ClosestR=	138313848	29344638	0,0,0	0,0,0
chr9	126949538	126949539	chr9	127070386	127070387	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=23],[Manta_PE=4,Manta_SR=18]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RALGPS1;DisruptR=RALGPS1;ClosestL=;ClosestR=ANGPTL2	138313848	138313848	22,126949537,127070386	0,0,0
chr9	129439237	129439238	chr12	110740607	110740608	TRA	NA	+	+	[Manta_PE=7,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AL353803.2;DisruptR=PPP1CC;ClosestL=AL353803.1;ClosestR=AC144522.1	138313848	112325530	0,0,0	0,0,0
chr9	131564960	131564961	chr13	24968358	24968359	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=28],[Manta_PE=24,Manta_SR=22]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=TPTE2P1;ClosestL=PRRT1B;ClosestR=	138313848	24952906	20,131564960,24968358	0,0,0
chr10	73043	73044	chr12	68509747	68509748	TRA	NA	+	+	[Svaba_SR=18,Svaba_PE=13],[Manta_PE=16,Manta_SR=14],[Lumpy_PE=9,Lumpy_SR=9]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TUBB8;DisruptR=;ClosestL=IL9RP2;ClosestR=	10287	67923116	13,73044,68509748	0,0,0
chr10	6816583	6816584	chr17	67550458	67550459	TRA	NA	-	-	[Lumpy_PE=2,Lumpy_SR=2]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC00707;DisruptR=PITPNC1;ClosestL=;ClosestR=	3411102	67102560	3,6816595,67550441	0,0,0
chr10	14933901	14933902	chr10	15104285	15104286	DEL	NA	+	-	[Manta_PE=2,Manta_SR=5]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=DCLRE1C;DisruptR=RPP38,NMT2;Fusion=NMT2+DCLRE1C;ClosestL=;ClosestR=C10orf111	23965103	23965103	4,14933903,15104285	0,0,0
chr10	23965110	23965111	chr10	27758065	27758066	DUP	NA	-	+	[Svaba_SR=26,Svaba_PE=23],[Manta_PE=17,Manta_SR=20],[Lumpy_PE=15,Lumpy_SR=17]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ABI1|Tier1;DisruptL=KIAA1217;DisruptR=MKX-AS1;Fusion=MKX-AS1+KIAA1217;ClosestL=;ClosestR=MKX	23965104	27758014	17,23965110,27758066	0,0,0
chr10	29469448	29469449	chr10	29471183	29471184	DEL	NA	+	-	[Svaba_SR=11,Svaba_PE=11],[Manta_PE=11,Manta_SR=10],[Lumpy_PE=7,Lumpy_SR=4]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SVIL-AS1,SVIL;DisruptR=SVIL-AS1,SVIL;ClosestL=;ClosestR=	29240716	29240716	9,29469450,29471177	0,0,0
chr10	38955179	38955180	chr22	25537608	25537609	TRA	NA	+	+	[Manta_PE=4,Manta_SR=5],[Lumpy_PE=2,Lumpy_SR=4]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=CRYBB2P1	39580116	24015969	4,38955181,25537609	0,0,0
chr10	43243169	43243170	chr10	43243707	43243708	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RASGEF1A;DisruptR=RASGEF1A;ClosestL=;ClosestR=	39580117	39580117	0,0,0	0,0,0
chr10	50989426	50989427	chr10	51034007	51034008	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=23],[Manta_PE=20,Manta_SR=60],[Lumpy_PE=45,Lumpy_SR=46]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=PRKG1;ClosestL=PRKG1;ClosestR=	39580117	39580117	17,50989429,51034008	0,0,0
chr10	50989426	50989427	chr10	51269465	51269466	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=32],[Manta_PE=27,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=PRKG1;ClosestL=PRKG1;ClosestR=	39580117	39580117	0,0,0	0,0,0
chr10	51033383	51033384	chr10	51269492	51269493	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=28],[Manta_PE=13,Manta_SR=48],[Lumpy_PE=13,Lumpy_SR=16]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PRKG1;DisruptR=PRKG1;ClosestL=;ClosestR=	39580117	39580117	32,51033385,51269619	0,0,0
chr10	51033894	51033895	chr10	51269618	51269619	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PRKG1;DisruptR=PRKG1;ClosestL=;ClosestR=	39580117	39580117	0,0,0	0,0,0
chr10	51349436	51349437	chr17	20111624	20111625	TRA	NA	+	-	[Manta_PE=0,Manta_SR=26],[Lumpy_PE=2,Lumpy_SR=17]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=SPECC1|Tier2;DisruptL=PRKG1;DisruptR=SPECC1;Fusion=PRKG1-SPECC1;ClosestL=;ClosestR=KCTD9P1	39580117	21658447	4,51349438,20111624	0,0,0
chr10	52646823	52646824	chr10	52650698	52650699	DEL	NA	+	-	[Svaba_SR=31,Svaba_PE=27],[Manta_PE=22,Manta_SR=27],[Lumpy_PE=8,Lumpy_SR=19]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC074327.1;DisruptR=AC074327.1;ClosestL=;ClosestR=	63904755	63904755	20,52646827,52650698	0,0,0
chr10	54306934	54306935	chr10	54494396	54494397	DEL	NA	+	-	[Svaba_SR=25,Svaba_PE=25],[Manta_PE=22,Manta_SR=21],[Lumpy_PE=13,Lumpy_SR=18]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=PCDH15;DisruptR=PCDH15,AL353784.1;ClosestL=;ClosestR=	63904755	63904755	18,54306933,54494396	0,0,0
chr10	87097352	87097353	chr10	87201988	87201989	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=35],[Manta_PE=31,Manta_SR=24],[Lumpy_PE=22,Lumpy_SR=3]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SHLD2;DisruptR=;ClosestL=GLUD1;ClosestR=NUTM2A-AS1	63904756	63904756	21,87097352,87201988	0,0,0
chr10	102637238	102637239	chr10	102638085	102638086	DUP	NA	-	+	[Svaba_SR=19,Svaba_PE=20],[Manta_PE=4,Manta_SR=17],[Lumpy_PE=4,Lumpy_SR=11]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=SUFU;ClosestR=TRIM8	133787316	133787316	12,102637237,102638086	0,0,0
chr10	105020094	105020095	chr10	105041776	105041777	DEL	NA	+	-	[Svaba_SR=14,Svaba_PE=16],[Manta_PE=13,Manta_SR=12],[Lumpy_PE=11,Lumpy_SR=11]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=SORCS3;DisruptR=SORCS3;ClosestL=;ClosestR=	133787316	133787316	11,105020091,105041776	0,0,0
chr10	118059368	118059369	chr10	118078970	118078971	DEL	NA	+	-	[Svaba_SR=9,Svaba_PE=10],[Manta_PE=11,Manta_SR=9],[Lumpy_PE=7,Lumpy_SR=8]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CASC2;DisruptR=CASC2;ClosestL=RAB11FIP2;ClosestR=	133787316	133787316	9,118059365,118078970	0,0,0
chr10	124466719	124466720	chr10	124471620	124471621	DEL	NA	+	-	[Manta_PE=17,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LHPP;DisruptR=LHPP;ClosestL=NKX1-2;ClosestR=RPS10P18	133787316	133787316	0,0,0	0,0,0
chr10	126525712	126525713	chr10	126567394	126567395	INV	NA	-	-	[Svaba_SR=19,Svaba_PE=21],[Manta_PE=19,Manta_SR=15],[Lumpy_PE=13,Lumpy_SR=12]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=C10orf90;DisruptR=C10orf90;ClosestL=;ClosestR=	133787316	133787316	11,126525711,126567394	0,0,0
chr10	126526972	126526973	chr10	126555979	126555980	DUP	NA	-	+	[Svaba_SR=21,Svaba_PE=24],[Manta_PE=20,Manta_SR=18],[Lumpy_PE=17,Lumpy_SR=13]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=C10orf90;DisruptR=C10orf90;ClosestL=;ClosestR=	133787316	133787316	16,126526971,126555981	0,0,0
chr11	6030233	6030234	chr11	7289788	7289789	INV	NA	-	-	[Svaba_SR=54,Svaba_PE=43],[Manta_PE=59,Manta_SR=53],[Lumpy_PE=36,Lumpy_SR=38]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=OR56A1;DisruptR=SYT9;Fusion=OR56A1+SYT9;ClosestL=RNA5SP329;ClosestR=	4827728	7289778	35,6030230,7289788	0,0,0
chr11	6378402	6378403	chr11	54541035	54541036	INV	NA	+	+	[Svaba_SR=0,Svaba_PE=43],[Manta_PE=45,Manta_SR=27],[Lumpy_PE=39,Lumpy_SR=16]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=MYOD1|Tier1,FANCF|Tier1,WT1|Tier1,LMO2|Tier1,CREB3L1|Tier1,DDB2|Tier1,LMO1|Tier1,EXT2|Tier1;DisruptL=;DisruptR=;ClosestL=SMPD1;ClosestR=	7289777	54537483	0,0,0	0,0,0
chr11	8415293	8415294	chr11	8417394	8417395	DEL	NA	+	-	[Svaba_SR=25,Svaba_PE=27],[Manta_PE=25,Manta_SR=24],[Lumpy_PE=20,Lumpy_SR=14]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=STK33;DisruptR=STK33;ClosestL=;ClosestR=	7844447	7844447	16,8415300,8417393	0,0,0
chr11	10522055	10522056	chr11	36593163	36593164	DEL	NA	+	-	[Svaba_SR=48,Svaba_PE=58],[Manta_PE=51,Manta_SR=46],[Lumpy_PE=35,Lumpy_SR=35]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=MYOD1|Tier1,FANCF|Tier1,WT1|Tier1,LMO2|Tier1;DisruptL=RNF141;DisruptR=RAG2;Fusion=RAG2+RNF141;ClosestL=MTRNR2L8;ClosestR=RAG1	10522051	36593150	34,10522054,36593163	0,0,0
chr11	11283180	11283181	chr11	39290286	39290287	DUP	NA	-	+	[Svaba_SR=48,Svaba_PE=58],[Manta_PE=55,Manta_SR=44],[Lumpy_PE=49,Lumpy_SR=30]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=MYOD1|Tier1,FANCF|Tier1,WT1|Tier1,LMO2|Tier1;DisruptL=GALNT18;DisruptR=;ClosestL=;ClosestR=	11283094	39290297	40,11283185,39290287	0,0,0
chr11	12343695	12343696	chr11	49740754	49740755	INV	NA	+	+	[Svaba_SR=40,Svaba_PE=42],[Manta_PE=43,Manta_SR=34],[Lumpy_PE=34,Lumpy_SR=26]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MYOD1|Tier1,FANCF|Tier1,WT1|Tier1,LMO2|Tier1,CREB3L1|Tier1,DDB2|Tier1,EXT2|Tier1;DisruptL=MICAL2;DisruptR=AC136759.1;ClosestL=;ClosestR=	12343416	49740713	27,12343696,49740765	0,0,0
chr11	18360996	18360997	chr11	18393125	18393126	DEL	NA	+	-	[Svaba_SR=18,Svaba_PE=22],[Manta_PE=22,Manta_SR=15],[Lumpy_PE=14,Lumpy_SR=10]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=GTF2H1;DisruptR=;ClosestL=;ClosestR=LDHA	12343416	12343416	15,18360997,18393125	0,0,0
chr11	47996838	47996839	chr11	51712926	51712927	INV	NA	-	-	[Manta_PE=3,Manta_SR=20]	manta	HCC-1143_80--HCC-1143BL_40	known=;gap;DisruptL=PTPRJ;DisruptR=;ClosestL=PTPRJ-AS1;ClosestR=	48860163	49740713	24,47996839,51712926	0,0,0
chr11	48037649	48037650	chr11	48243138	48243139	INV	NA	+	+	[Svaba_SR=37,Svaba_PE=51],[Manta_PE=58,Manta_SR=31],[Lumpy_PE=56,Lumpy_SR=17]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=PTPRJ;DisruptR=;ClosestL=;ClosestR=OR4X2	48860163	48860163	27,48037651,48243139	0,0,0
chr11	48423266	48423267	chr11	48845188	48845189	INV	NA	-	-	[Svaba_SR=30,Svaba_PE=27],[Manta_PE=36,Manta_SR=26],[Lumpy_PE=27,Lumpy_SR=12]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=OR4C2P;ClosestR=	48860163	48860163	24,48423265,48845188	0,0,0
chr11	58190284	58190285	chr11	62369331	62369332	DEL	NA	+	-	[Svaba_SR=40,Svaba_PE=51],[Manta_PE=39,Manta_SR=36]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=FEN1|Tier2,SDHAF2|Tier1;DisruptL=OR9Q2;DisruptR=ASRGL1;Fusion=OR9Q2+ASRGL1;ClosestL=OR9Q1;ClosestR=RCC2P6	58828468	60292996	29,58190284,62369331	0,0,0
chr11	58902609	58902610	chrX	56991096	56991097	TRA	NA	-	-	[Svaba_SR=34,Svaba_PE=27],[Manta_PE=28,Manta_SR=30]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=GLYATL2;DisruptR=SPIN3;ClosestL=GLYATL1;ClosestR=AL139397.1	58828469	56991084	0,0,0	0,0,0
chr11	59869578	59869579	chr11	59872428	59872429	INV	NA	-	-	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=TCN1;ClosestR=TCN1	59869483	59869483	0,0,0	0,0,0
chr11	59869579	59869580	chr11	65511687	65511688	DUP	NA	-	+	[Svaba_SR=34,Svaba_PE=13],[Manta_PE=11,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=FEN1|Tier2,MEN1|Tier1,MALAT1|Tier2,SDHAF2|Tier1;DisruptL=;DisruptR=;ClosestL=TCN1;ClosestR=SNRPGP19	59869483	65505150	0,0,0	0,0,0
chr11	59869579	59869580	chr11	68509921	68509922	DUP	NA	-	+	[Svaba_SR=30,Svaba_PE=7],[Manta_PE=7,Manta_SR=25]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=FEN1|Tier2,MEN1|Tier1,MALAT1|Tier2,SDHAF2|Tier1;DisruptL=;DisruptR=PPP6R3;ClosestL=TCN1;ClosestR=	59869483	69098161	0,0,0	0,0,0
chr11	59871620	59871621	chr11	68509680	68509681	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=FEN1|Tier2,MEN1|Tier1,MALAT1|Tier2,SDHAF2|Tier1;DisruptL=;DisruptR=PPP6R3;ClosestL=TCN1;ClosestR=	59869483	69098161	0,0,0	0,0,0
chr11	60085406	60085407	chr13	110454732	110454733	TRA	NA	-	-	[Svaba_SR=22,Svaba_PE=22],[Manta_PE=24,Manta_SR=21],[Lumpy_PE=13,Lumpy_SR=12]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=COL4A2;ClosestL=MS4A2;ClosestR=COL4A2-AS2	60292995	110418576	14,60085405,110454726	0,0,0
chr11	60279269	60279270	chr11	62579531	62579532	INV	NA	+	+	[Svaba_SR=34,Svaba_PE=39],[Manta_PE=41,Manta_SR=30],[Lumpy_PE=37,Lumpy_SR=26]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FEN1|Tier2,SDHAF2|Tier1;DisruptL=;DisruptR=AP002990.1,TUT1;ClosestL=MS4A4A;ClosestR=EEF1G	60292995	60292996	28,60279270,62579532	0,0,0
chr11	60292660	60292661	chr11	60293218	60293219	INV	NA	+	+	[Svaba_SR=18,Svaba_PE=24],[Manta_PE=23,Manta_SR=14],[Lumpy_PE=19,Lumpy_SR=9]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MS4A4A;DisruptR=MS4A4A;ClosestL=;ClosestR=	60292995	60292996	12,60292660,60293219	0,0,0
chr11	63930760	63930761	chr11	63934315	63934316	INV	NA	+	+	[Svaba_SR=36,Svaba_PE=24],[Manta_PE=25,Manta_SR=31]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=NAA40;ClosestR=NAA40	65505149	65505149	28,63930729,63934316	0,0,0
chr11	63930764	63930765	chr11	63935811	63935812	INV	NA	-	-	[Manta_PE=83,Manta_SR=60],[Lumpy_PE=52,Lumpy_SR=35]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;ClosestL=NAA40;ClosestR=NAA40	65505149	65505149	47,63930766,63935810	0,0,0
chr11	63930769	63930770	chr11	63931436	63931437	INV	NA	+	+	[Svaba_SR=0,Svaba_PE=47]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=NAA40;ClosestR=NAA40	65505149	65505149	0,0,0	0,0,0
chr11	65505166	65505167	chr11	67780973	67780974	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MALAT1;DisruptR=;ClosestL=RF01684;ClosestR=ALG1L8P	65505150	67782749	0,0,0	0,0,0
chr11	65505167	65505168	chr11	68509680	68509681	DUP	NA	-	+	[Svaba_SR=46,Svaba_PE=9],[Manta_PE=9,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MALAT1;DisruptR=PPP6R3;Fusion=PPP6R3+MALAT1;ClosestL=RF01684;ClosestR=	65505150	69098161	0,0,0	0,0,0
chr11	65511293	65511294	chr11	68509503	68509504	INV	NA	-	-	[Svaba_SR=39,Svaba_PE=0]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=PPP6R3;ClosestL=SNRPGP19;ClosestR=	65505150	69098161	0,0,0	0,0,0
chr11	65511293	65511294	chr12	33652636	33652637	TRA	NA	-	-	[Svaba_SR=24,Svaba_PE=0],[Manta_PE=20,Manta_SR=21],[Lumpy_PE=10,Lumpy_SR=21]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=SNRPGP19;ClosestR=	65505150	56255606	18,65511296,33652636	0,0,0
chr11	65511687	65511688	chr11	68509833	68509834	DEL	NA	+	-	[Manta_PE=4,Manta_SR=17]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=PPP6R3;ClosestL=SNRPGP19;ClosestR=	65505150	69098161	0,0,0	0,0,0
chr11	67780632	67780633	chr12	125881063	125881064	TRA	NA	+	-	[Svaba_SR=25,Svaba_PE=17],[Manta_PE=20,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=4]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=ALG1L8P;ClosestR=AC005252.1	67782749	125881976	0,0,0	0,0,0
chr11	67780880	67780881	chr12	33653292	33653293	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=11],[Manta_PE=11,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=ALG1L8P;ClosestR=	67782749	56255606	0,0,0	0,0,0
chr11	68509503	68509504	chr12	33653292	33653293	TRA	NA	-	+	[Svaba_SR=16,Svaba_PE=14],[Manta_PE=15,Manta_SR=14],[Lumpy_PE=11,Lumpy_SR=10]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PPP6R3;DisruptR=;ClosestL=;ClosestR=	69098161	56255606	11,68509504,33653293	0,0,0
chr11	68509840	68509841	chr12	33653117	33653118	TRA	NA	+	-	[Manta_PE=2,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PPP6R3;DisruptR=;ClosestL=;ClosestR=	69098161	56255606	0,0,0	0,0,0
chr11	69098215	69098216	chr11	69099668	69099669	INV	NA	-	-	[Svaba_SR=113,Svaba_PE=106],[Manta_PE=197,Manta_SR=168],[Lumpy_PE=132,Lumpy_SR=128]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TPCN2;DisruptR=TPCN2;ClosestL=AP003071.1;ClosestR=AP003071.1	69098162	69098162	0,0,0	0,0,0
chr11	69189129	69189130	chr12	108227528	108227529	TRA	NA	-	-	[Manta_PE=10,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=WSCD2;ClosestL=AP003071.2;ClosestR=	69098162	112325530	3,69189098,108227720	0,0,0
chr11	69757101	69757102	chr11	69769201	69769202	INV	NA	+	+	[Svaba_SR=0,Svaba_PE=86],[Manta_PE=108,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=FGF4;ClosestR=FGF4	69779346	69779346	0,0,0	0,0,0
chr11	69757101	69757102	chr14	21263990	21263991	TRA	NA	+	+	[Svaba_SR=137,Svaba_PE=62],[Manta_PE=68,Manta_SR=142],[Lumpy_PE=17,Lumpy_SR=106]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=HNRNPC;ClosestL=FGF4;ClosestR=	69779346	21264197	71,69757103,21263991	0,0,0
chr11	69769200	69769201	chr14	21263862	21263863	TRA	NA	+	-	[Svaba_SR=133,Svaba_PE=49],[Manta_PE=56,Manta_SR=118],[Lumpy_PE=16,Lumpy_SR=101]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=HNRNPC;ClosestL=FGF4;ClosestR=	69779346	21264197	68,69769197,21263862	0,0,0
chr11	73534605	73534606	chr11	73698866	73698867	DUP	NA	-	+	[Svaba_SR=8,Svaba_PE=23],[Manta_PE=23,Manta_SR=0],[Lumpy_PE=22,Lumpy_SR=1]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FAM168A;DisruptR=RAB6A;Fusion=FAM168A+RAB6A;ClosestL=;ClosestR=	73059915	73059915	0,0,0	0,0,0
chr11	76901510	76901511	chr22	28499618	28499619	TRA	NA	+	-	[Svaba_SR=28,Svaba_PE=14],[Manta_PE=14,Manta_SR=28],[Lumpy_PE=11,Lumpy_SR=16]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ACER3;DisruptR=TTC28;ClosestL=;ClosestR=	78640369	29344638	0,0,0	0,0,0
chr11	80765276	80765277	chrX	87668752	87668753	TRA	NA	+	+	[Manta_PE=7,Manta_SR=8],[Lumpy_PE=2,Lumpy_SR=7]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=KLHL4;ClosestL=AP002759.1;ClosestR=	80765305	87101847	7,80765278,87668753	0,0,0
chr11	121197469	121197470	chr11	121472976	121472977	DUP	NA	-	+	[Svaba_SR=20,Svaba_PE=13],[Manta_PE=14,Manta_SR=14],[Lumpy_PE=10,Lumpy_SR=3]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=SORL1;ClosestL=TECTA;ClosestR=AP000977.1	121197407	121473002	10,121197470,121472977	0,0,0
chr12	25346053	25346054	chr12	25347333	25347334	DUP	NA	-	+	[Svaba_SR=17,Svaba_PE=22],[Manta_PE=20,Manta_SR=17],[Lumpy_PE=17,Lumpy_SR=13]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	41087	41087	14,25346052,25347334	0,0,0
chr12	35947609	35947610	chr12	36918488	36918489	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	56255606	56255606	0,0,0	0,0,0
chr12	37654140	37654141	chr12	37658683	37658684	DUP	NA	-	+	[Svaba_SR=22,Svaba_PE=5],[Manta_PE=18,Manta_SR=21],[Lumpy_PE=24,Lumpy_SR=7]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	56255606	56255606	0,0,0	0,0,0
chr12	37654199	37654200	chr12	37658674	37658675	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=7],[Lumpy_PE=4,Lumpy_SR=8]	svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	56255606	56255606	11,37654199,37658664	0,0,0
chr12	37654199	37654200	chr12	37658947	37658948	INV	NA	+	+	[Svaba_SR=34,Svaba_PE=11],[Manta_PE=6,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	56255606	56255606	0,0,0	0,0,0
chr12	37654605	37654606	chr12	37658765	37658766	INV	NA	-	-	[Svaba_SR=18,Svaba_PE=17],[Manta_PE=22,Manta_SR=13],[Lumpy_PE=23,Lumpy_SR=9]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	56255606	56255606	10,37654609,37658765	0,0,0
chr12	37654614	37654615	chr12	37658938	37658939	DEL	NA	+	-	[Svaba_SR=13,Svaba_PE=0],[Manta_PE=24,Manta_SR=16],[Lumpy_PE=13,Lumpy_SR=8]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	56255606	56255606	14,37654612,37658938	0,0,0
chr12	37656929	37656930	chr12	37658031	37658032	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=10]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	56255606	56255606	14,37656927,37658031	0,0,0
chr12	37656929	37656930	chr12	38268739	38268740	INV	NA	+	+	[Svaba_SR=31,Svaba_PE=19],[Manta_PE=21,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=RF00019	56255606	56255606	0,0,0	0,0,0
chr12	37657372	37657373	chr12	38301158	38301159	INV	NA	-	-	[Svaba_SR=23,Svaba_PE=21],[Manta_PE=23,Manta_SR=20],[Lumpy_PE=15,Lumpy_SR=15]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=ALG10B	56255606	56255606	18,37657369,38301158	0,0,0
chr12	37658101	37658102	chr12	38268739	38268740	INV	NA	+	+	[Svaba_SR=16,Svaba_PE=4]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=RF00019	56255606	56255606	7,37658097,38268740	0,0,0
chr12	49263676	49263677	chr12	49265087	49265088	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=29],[Manta_PE=27,Manta_SR=18],[Lumpy_PE=21,Lumpy_SR=12]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TUBA1C,AC010173.1;DisruptR=TUBA1C;ClosestL=AC125611.3;ClosestR=AC125611.3	56255606	56255606	14,49263672,49265087	0,0,0
chr12	56255681	56255682	chr12	61144864	61144865	DUP	NA	-	+	[Svaba_SR=60,Svaba_PE=71],[Manta_PE=63,Manta_SR=54],[Lumpy_PE=52,Lumpy_SR=39]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=NAB2|Tier1,GLI1|Tier2,DDIT3|Tier1,CDK4|Tier1,NACA|Tier2,STAT6|Tier1,LRIG3|Tier1;DisruptL=ANKRD52;DisruptR=;ClosestL=COQ10A;ClosestR=	56255607	61144794	37,56255678,61144868	0,0,0
chr12	65713913	65713914	chr12	112325570	112325571	INV	NA	-	-	[Svaba_SR=100,Svaba_PE=147],[Manta_PE=358,Manta_SR=343],[Lumpy_PE=203,Lumpy_SR=299]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=BTG1|Tier1,PTPRB|Tier1,USP44|Tier2,SH2B3|Tier1,HMGA2|Tier1,MDM2|Tier1,CHST11|Tier2,ALDH2|Tier2;DisruptL=;DisruptR=HECTD4;ClosestL=;ClosestR=AC004217.2	65713850	112325531	2,65713911,112325575	0,0,0
chr12	65856872	65856873	chr12	67766189	67766190	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=20],[Manta_PE=16,Manta_SR=20],[Lumpy_PE=8,Lumpy_SR=20]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=HMGA2|Tier1;DisruptL=AC090673.1,HMGA2;DisruptR=;ClosestL=;ClosestR=AC022513.1	65713850	67923115	18,65856873,67766189	0,0,0
chr12	66145833	66145834	chr12	66682452	66682453	DUP	NA	-	+	[Svaba_SR=30,Svaba_PE=40],[Manta_PE=34,Manta_SR=25],[Lumpy_PE=26,Lumpy_SR=23]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC078927.1,TMBIM4;DisruptR=GRIP1;Fusion=AC078927.1+GRIP1|TMBIM4+GRIP1;ClosestL=LLPH-DT;ClosestR=	65713850	65713850	22,66145834,66682453	0,0,0
chr12	66362648	66362649	chr12	68497810	68497811	DUP	NA	-	+	[Svaba_SR=51,Svaba_PE=65],[Manta_PE=58,Manta_SR=44],[Lumpy_PE=53,Lumpy_SR=31]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=GRIP1;DisruptR=;ClosestL=HELB;ClosestR=AC008033.2	65713850	67923116	32,66362649,68497811	0,0,0
chr12	66410668	66410669	chr12	69873475	69873476	DEL	NA	+	-	[Svaba_SR=12,Svaba_PE=22],[Manta_PE=28,Manta_SR=20],[Lumpy_PE=23,Lumpy_SR=14]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=MDM2|Tier1;DisruptL=GRIP1;DisruptR=MYRFL;ClosestL=;ClosestR=AC025263.2	65713850	69869147	19,66410665,69873475	0,0,0
chr12	66453482	66453483	chr12	68613971	68613972	DEL	NA	+	-	[Svaba_SR=65,Svaba_PE=61],[Manta_PE=54,Manta_SR=51],[Lumpy_PE=33,Lumpy_SR=39]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=GRIP1;DisruptR=RAP1B;ClosestL=;ClosestR=RPL10P12	65713850	67923116	40,66453484,68613971	0,0,0
chr12	67114681	67114682	chr21	32343522	32343523	TRA	NA	-	-	[Svaba_SR=47,Svaba_PE=5]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=URB1;ClosestL=RAB11AP2;ClosestR=	67923115	32739659	0,0,0	0,0,0
chr12	67919941	67919942	chr12	67923109	67923110	INV	NA	+	+	[Svaba_SR=84,Svaba_PE=88],[Manta_PE=90,Manta_SR=78],[Lumpy_PE=76,Lumpy_SR=62]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;ClosestL=LINC01479;ClosestR=LINC01479	67923115	67923115	24,67919943,67923110	0,0,0
chr12	69782621	69782622	chr12	69869191	69869192	DEL	NA	+	-	[Svaba_SR=163,Svaba_PE=187],[Manta_PE=168,Manta_SR=149],[Lumpy_PE=105,Lumpy_SR=120]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RAB3IP;DisruptR=MYRFL;Fusion=RAB3IP+MYRFL;ClosestL=AC025263.2;ClosestR=AC025263.2	69782593	69869147	80,69782622,69869191	0,0,0
chr12	69853157	69853158	chr12	69853921	69853922	DEL	NA	+	-	[Svaba_SR=4,Svaba_PE=0]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC025263.2,MYRFL;DisruptR=AC025263.2,MYRFL;Fusion=AC025263.2+MYRFL|MYRFL+AC025263.2;ClosestL=;ClosestR=	69869146	69869146	0,0,0	0,0,0
chr12	69967248	69967249	chr12	70003771	70003772	INV	NA	+	+	[Svaba_SR=18,Svaba_PE=20],[Manta_PE=21,Manta_SR=11],[Lumpy_PE=18,Lumpy_SR=9]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC025159.1;DisruptR=AC025159.1;ClosestL=MYRFL;ClosestR=	69869147	69869147	11,69967248,70003772	0,0,0
chr12	71972105	71972106	chr12	71993496	71993497	DUP	NA	-	+	[Svaba_SR=23,Svaba_PE=22],[Manta_PE=18,Manta_SR=20],[Lumpy_PE=16,Lumpy_SR=12]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TPH2;DisruptR=TPH2;ClosestL=;ClosestR=	71964314	71964314	0,0,0	0,0,0
chr12	71975432	71975433	chr12	72007830	72007831	INV	NA	-	-	[Svaba_SR=64,Svaba_PE=66],[Manta_PE=63,Manta_SR=52],[Lumpy_PE=43,Lumpy_SR=36]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TPH2;DisruptR=TPH2;ClosestL=;ClosestR=	71964314	71964314	39,71975433,72007830	0,0,0
chr12	72510655	72510656	chr12	72511895	72511896	INV	NA	+	+	[Svaba_SR=118,Svaba_PE=139],[Manta_PE=144,Manta_SR=113],[Lumpy_PE=120,Lumpy_SR=87]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TRHDE;DisruptR=TRHDE;ClosestL=;ClosestR=	72511936	72511936	71,72510657,72511896	0,0,0
chr12	72534503	72534504	chr12	72535081	72535082	DUP	NA	-	+	[Svaba_SR=15,Svaba_PE=16],[Manta_PE=14,Manta_SR=14],[Lumpy_PE=12,Lumpy_SR=11]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TRHDE;DisruptR=TRHDE;ClosestL=;ClosestR=	72511937	72511937	12,72534504,72535082	0,0,0
chr12	82997175	82997176	chr13	109382851	109382852	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TMTC2;DisruptR=;ClosestL=;ClosestR=LINC00399	72511937	110418575	3,82997423,109382778	5,82997353,109382816
chr12	96149120	96149121	chr12	96166173	96166174	DEL	NA	+	-	[Svaba_SR=25,Svaba_PE=25],[Manta_PE=22,Manta_SR=23],[Lumpy_PE=16,Lumpy_SR=17]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=LINC02452;ClosestL=LINC02452;ClosestR=	112325530	112325530	20,96149120,96166173	0,0,0
chr12	101739295	101739296	chr12	101984856	101984857	DUP	NA	-	+	[Svaba_SR=24,Svaba_PE=25],[Manta_PE=21,Manta_SR=15],[Lumpy_PE=18,Lumpy_SR=10]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SYCP3,CHPT1;DisruptR=DRAM1;Fusion=DRAM1+CHPT1;ClosestL=GNPTAB;ClosestR=	112325530	112325530	12,101739295,101984857	0,0,0
chr12	112316935	112316936	chr12	112384855	112384856	DUP	NA	-	+	[Svaba_SR=160,Svaba_PE=194],[Manta_PE=171,Manta_SR=145],[Lumpy_PE=151,Lumpy_SR=56]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=HECTD4;DisruptR=;ClosestL=AC004217.2;ClosestR=HECTD4	112325530	112386380	75,112316936,112384856	0,0,0
chr12	112317527	112317528	chr12	112386389	112386390	INV	NA	+	+	[Svaba_SR=154,Svaba_PE=128],[Manta_PE=178,Manta_SR=156],[Lumpy_PE=155,Lumpy_SR=129]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=HECTD4;DisruptR=;ClosestL=AC004217.2;ClosestR=HECTD4	112325530	112386381	82,112317526,112386390	0,0,0
chr12	112383548	112383549	chr12	112384065	112384066	DEL	NA	+	-	[Svaba_SR=4,Svaba_PE=0]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=HECTD4;ClosestR=HECTD4	112386380	112386380	0,0,0	0,0,0
chr13	22965509	22965510	chr13	24390643	24390644	DUP	NA	-	+	[Manta_PE=4,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=CYCSP33	23788056	24952905	0,0,0	0,0,0
chr13	22966274	22966275	chr13	24391077	24391078	DEL	NA	+	-	[Manta_PE=5,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=CYCSP33	23788056	24952905	0,0,0	0,0,0
chr13	25024466	25024467	chr13	25030471	25030472	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=22],[Manta_PE=23,Manta_SR=21],[Lumpy_PE=17,Lumpy_SR=9]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;ClosestL=AL590099.1;ClosestR=AL590099.1	24952906	24952906	18,25024465,25030471	0,0,0
chr13	28880457	28880458	chr13	98509424	98509425	DEL	NA	+	-	[Svaba_SR=47,Svaba_PE=66],[Manta_PE=58,Manta_SR=43],[Lumpy_PE=38,Lumpy_SR=36]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;gap;Cancer_census=CYSLTR2|Tier2,SOX21|Tier2,BRCA2|Tier1,LHFP|Tier2,FOXO1|Tier1,RB1|Tier1,NBEA|Tier2,LCP1|Tier2,GPC5|Tier2;DisruptL=MTUS2;DisruptR=STK24;ClosestL=;ClosestR=	28880402	98509395	37,28880457,98509424	0,0,0
chr13	97331894	97331895	chr13	97689069	97689070	DEL	NA	+	-	[Svaba_SR=31,Svaba_PE=28],[Manta_PE=19,Manta_SR=24],[Lumpy_PE=16,Lumpy_SR=15]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MBNL2;DisruptR=;ClosestL=;ClosestR=AL359502.1	97331911	97689209	18,97331894,97689069	0,0,0
chr13	101085680	101085681	chr13	101107648	101107649	DEL	NA	+	-	[Svaba_SR=11,Svaba_PE=23],[Manta_PE=25,Manta_SR=9],[Lumpy_PE=19,Lumpy_SR=7]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=NALCN;DisruptR=NALCN;ClosestL=;ClosestR=	98509395	98509395	9,101085680,101107648	0,0,0
chr13	102238357	102238358	chr21	18481781	18481782	TRA	NA	-	+	[Svaba_SR=4,Svaba_PE=8],[Manta_PE=10,Manta_SR=5],[Lumpy_PE=9,Lumpy_SR=3]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FGF14;DisruptR=TMPRSS15,AL109763.1;Fusion=FGF14-TMPRSS15|FGF14-AL109763.1;ClosestL=;ClosestR=	98509395	18484759	4,102238356,18481782	0,0,0
chr13	104720020	104720021	chr21	17226145	17226146	TRA	NA	-	+	[Lumpy_PE=2,Lumpy_SR=3]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=NEK4P1	107326494	17474345	3,104720018,17226145	0,0,0
chr13	107326514	107326515	chr13	107327081	107327082	INV	NA	-	-	[Svaba_SR=21,Svaba_PE=15]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FAM155A;DisruptR=FAM155A;ClosestL=SNORD31B;ClosestR=SNORD31B	107326495	107326495	4,107326511,107327078	0,0,0
chr13	107326584	107326585	chr18	3047624	3047625	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=13]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FAM155A;DisruptR=;ClosestL=SNORD31B;ClosestR=MYOM1	107326495	3047604	7,107326584,3047570	0,0,0
chr13	107327055	107327056	chr18	3047589	3047590	TRA	NA	-	-	[Manta_PE=20,Manta_SR=0]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FAM155A;DisruptR=;ClosestL=SNORD31B;ClosestR=MYOM1	107326495	3047603	0,0,0	0,0,0
chr13	107559859	107559860	chr13	108859484	108859485	DUP	NA	-	+	[Lumpy_PE=9,Lumpy_SR=4]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FAM155A;DisruptR=MYO16;ClosestL=;ClosestR=	107326495	107326495	5,107559859,108859484	0,0,0
chr13	107560030	107560031	chr13	108859489	108859490	INV	NA	-	-	[Svaba_SR=21,Svaba_PE=19],[Manta_PE=20,Manta_SR=18],[Lumpy_PE=3,Lumpy_SR=16]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FAM155A;DisruptR=MYO16;Fusion=FAM155A+MYO16;ClosestL=;ClosestR=	107326495	107326495	17,107560032,108859489	0,0,0
chr13	107560301	107560302	chr13	108954298	108954299	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=27],[Manta_PE=23,Manta_SR=17],[Lumpy_PE=17,Lumpy_SR=13]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FAM155A;DisruptR=MYO16;ClosestL=;ClosestR=	107326495	110418575	16,107560301,108954298	0,0,0
chr13	108859285	108859286	chr13	108952396	108952397	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=0],[Manta_PE=15,Manta_SR=20]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR=	107326495	110418575	3,108859287,108952275	0,0,0
chr13	108859328	108859329	chr13	108952203	108952204	DUP	NA	-	+	[Svaba_SR=24,Svaba_PE=0],[Manta_PE=10,Manta_SR=19]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR=	107326495	110418575	13,108859329,108952204	0,0,0
chr13	108860016	108860017	chr13	108951977	108951978	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR=	107326495	110418575	0,0,0	0,0,0
chr14	20575192	20575193	chr14	21264283	21264284	DUP	NA	-	+	[Svaba_SR=35,Svaba_PE=44],[Manta_PE=34,Manta_SR=30],[Lumpy_PE=31,Lumpy_SR=24]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=HNRNPC;ClosestL=AL163195.3;ClosestR=	20575059	21264198	25,20575195,21264284	0,0,0
chr14	28611454	28611455	chr22	28669723	28669724	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=24]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC02300,TTC28;DisruptR=TTC28;Fusion=TTC28-LINC02300;ClosestL=EIF4A1P12;ClosestR=CHEK2	21264198	29344638	0,0,0	0,0,0
chr14	28611660	28611661	chr22	28669767	28669768	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=20],[Lumpy_PE=2,Lumpy_SR=28]	lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC02300,TTC28;DisruptR=TTC28;Fusion=LINC02300-TTC28;ClosestL=EIF4A1P12;ClosestR=CHEK2	21264198	29344638	10,28611556,28669768	0,0,0
chr14	32961999	32962000	chr14	32970923	32970924	DEL	NA	+	-	[Svaba_SR=80,Svaba_PE=86],[Manta_PE=83,Manta_SR=68],[Lumpy_PE=59,Lumpy_SR=44]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=NPAS3;DisruptR=NPAS3;ClosestL=;ClosestR=	41140316	41140316	44,32961999,32970923	0,0,0
chr14	41463251	41463252	chr14	41474102	41474103	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=18],[Manta_PE=17,Manta_SR=17],[Lumpy_PE=15,Lumpy_SR=2]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	41200381	41200381	0,0,0	0,0,0
chr14	81201605	81201606	chr14	81202852	81202853	DUP	NA	-	+	[Svaba_SR=11,Svaba_PE=19],[Manta_PE=19,Manta_SR=0],[Lumpy_PE=15,Lumpy_SR=8]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=GTF2A1;DisruptR=GTF2A1;ClosestL=SNORA79;ClosestR=SNORA79	91109906	91109906	9,81201605,81202853	0,0,0
chr14	91109951	91109952	chr14	91493414	91493415	DUP	NA	-	+	[Svaba_SR=49,Svaba_PE=54],[Manta_PE=49,Manta_SR=40],[Lumpy_PE=46,Lumpy_SR=32]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=DGLUCY;DisruptR=PPP4R3A;ClosestL=SNORA11B;ClosestR=	91109907	91493434	28,91109952,91493415	0,0,0
chr14	100903884	100903885	chrX	87668584	87668585	TRA	NA	-	-	[Svaba_SR=17,Svaba_PE=3],[Manta_PE=2,Manta_SR=14]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AL117190.1,MEG8;DisruptR=KLHL4;ClosestL=RF02146;ClosestR=	104243063	87101847	8,100903895,87668584	0,0,0
chr14	104243055	104243056	chr14	104326293	104326294	INV	NA	-	-	[Svaba_SR=106,Svaba_PE=124],[Manta_PE=123,Manta_SR=88],[Lumpy_PE=86,Lumpy_SR=73]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AL590079.1;DisruptR=;ClosestL=;ClosestR=	104243063	104243064	57,104243056,104326293	0,0,0
chr14	104704163	104704164	chr14	105433354	105433355	DUP	NA	-	+	[Svaba_SR=89,Svaba_PE=96],[Manta_PE=82,Manta_SR=82],[Lumpy_PE=68,Lumpy_SR=55]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=AKT1|Tier1;DisruptL=INF2;DisruptR=TEX22,MTA1;Fusion=TEX22+INF2|MTA1+INF2;ClosestL=AL583722.4;ClosestR=AL928654.1	104243064	105433357	54,104704159,105433355	0,0,0
chr14	105117762	105117763	chr14	105352505	105352506	DUP	NA	-	+	[Svaba_SR=43,Svaba_PE=61],[Manta_PE=53,Manta_SR=40],[Lumpy_PE=45,Lumpy_SR=35]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=PACS2;ClosestL=AL512356.2;ClosestR=AL928654.4	105433357	105433357	29,105117762,105352506	0,0,0
chr14	105893557	105893558	chr14	105902666	105902667	DUP	NA	-	+	[Manta_PE=4,Manta_SR=82]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC246787.2,IGHD5-18;DisruptR=IGHD5-12;Fusion=IGHD5-18+IGHD5-12;ClosestL=IGHD4-17;ClosestR=IGHD4-11	105433358	105433358	5,105893572,105902683	0,0,0
chr15	21545403	21545404	chr18	67194548	67194549	TRA	NA	+	+	[Svaba_SR=28,Svaba_PE=14]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC183088.1;ClosestR=	17083473	67194497	17,21545405,67194549	0,0,0
chr15	56746798	56746799	chr15	56751379	56751380	INV	NA	-	-	[Svaba_SR=41,Svaba_PE=45],[Manta_PE=49,Manta_SR=31],[Lumpy_PE=36,Lumpy_SR=24]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AC090517.4;DisruptR=AC090517.4;ClosestL=ZNF280D;ClosestR=ZNF280D	56746779	56746779	27,56746800,56751379	0,0,0
chr15	65803608	65803609	chr18	11294088	11294089	TRA	NA	-	+	[Svaba_SR=29,Svaba_PE=29],[Manta_PE=24,Manta_SR=25],[Lumpy_PE=18,Lumpy_SR=17]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RAB11A;DisruptR=;ClosestL=DENND4A;ClosestR=	65078752	11293418	22,65803604,11294089	0,0,0
chr15	72000221	72000222	chr15	72362565	72362566	DUP	NA	-	+	[Svaba_SR=55,Svaba_PE=71],[Manta_PE=70,Manta_SR=44],[Lumpy_PE=66,Lumpy_SR=32]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC022872.1,MYO9A;DisruptR=AC009690.1,HEXA;Fusion=MYO9A+AC009690.1|MYO9A+HEXA;ClosestL=;ClosestR=AC009690.2	72000144	72362589	32,72000222,72362566	0,0,0
chr15	76561965	76561966	chr16	67651996	67651997	TRA	NA	+	+	[Manta_PE=1,Manta_SR=18],[Lumpy_PE=5,Lumpy_SR=11]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SCAPER;DisruptR=CARMIL2;Fusion=CARMIL2-SCAPER;ClosestL=;ClosestR=ACD	72362590	90226217	11,76561967,67651997	0,0,0
chr15	84047235	84047236	chr15	84047818	84047819	DEL	NA	+	-	[Svaba_SR=47,Svaba_PE=42],[Manta_PE=30,Manta_SR=41],[Lumpy_PE=21,Lumpy_SR=28]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC027807.1;ClosestR=AC027807.1	72362590	72362590	33,84047237,84047817	0,0,0
chr16	187562	187563	chrY	56870831	56870832	TRA	NA	-	-	[Svaba_SR=34,Svaba_PE=3]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=Z69706.1;ClosestR=CTBP2P1	10005	-1	0,0,0	0,0,0
chr16	515531	515532	chr17	22058252	22058253	TRA	NA	+	+	[Svaba_SR=12,Svaba_PE=13],[Manta_PE=12,Manta_SR=9]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RAB11FIP3;DisruptR=;ClosestL=LINC00235;ClosestR=ABBA01006766.1	10005	22044138	6,515530,22058253	0,0,0
chr16	3191703	3191704	chr16	3228907	3228908	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=28],[Manta_PE=28,Manta_SR=22],[Lumpy_PE=19,Lumpy_SR=10]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AJ003147.2;DisruptR=ZNF200;ClosestL=AJ003147.1;ClosestR=AJ003147.2	10005	10005	0,0,0	0,0,0
chr16	24481252	24481253	chr16	24513939	24513940	DEL	NA	+	-	[Svaba_SR=48,Svaba_PE=68],[Manta_PE=64,Manta_SR=45],[Lumpy_PE=49,Lumpy_SR=21]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AC008938.1;DisruptR=;ClosestL=;ClosestR=AC008938.1	34502581	34502581	34,24481254,24513934	0,0,0
chr16	37750073	37750074	chr21	18585120	18585121	TRA	NA	-	+	[Svaba_SR=11,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=MIR548XHG;ClosestL=;ClosestR=	34596149	18484760	0,0,0	0,0,0
chr16	70232878	70232879	chr16	70281139	70281140	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=23],[Manta_PE=4,Manta_SR=19]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SMG1P7;DisruptR=AARS;Fusion=AARS+SMG1P7;ClosestL=EXOSC6;ClosestR=RN7SL279P	90226217	90226217	18,70232878,70281139	0,0,0
chr16	74657089	74657090	chr16	74659685	74659686	DEL	NA	+	-	[Manta_PE=4,Manta_SR=5],[Lumpy_PE=3,Lumpy_SR=4]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=RFWD3|Tier2;DisruptL=RFWD3;DisruptR=RFWD3;ClosestL=TMPOP2;ClosestR=TMPOP2	90226217	90226217	5,74657091,74659686	0,0,0
chr16	76745602	76745603	chr16	76759438	76759439	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=20],[Manta_PE=21,Manta_SR=23],[Lumpy_PE=13,Lumpy_SR=18]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC104151.1,AC106729.1;DisruptR=AC104151.1,AC106729.1;Fusion=AC104151.1+AC106729.1|AC106729.1+AC104151.1;ClosestL=;ClosestR=	90226217	90226217	21,76745604,76759438	0,0,0
chr16	89517377	89517378	chr16	89597850	89597851	DUP	NA	-	+	[Svaba_SR=13,Svaba_PE=0],[Manta_PE=20,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=4]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SPG7;DisruptR=;ClosestL=AC092123.1;ClosestR=CPNE7	90226217	90226217	6,89517378,89597851	0,0,0
chr17	1788505	1788506	chr17	35740201	35740202	INV	NA	-	-	[Svaba_SR=9,Svaba_PE=0],[Manta_PE=2,Manta_SR=16],[Lumpy_PE=2,Lumpy_SR=3]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=TP53|Tier1,USP6|Tier1,PER1|Tier1,FLCN|Tier1,RABEP1|Tier1,GAS7|Tier1,MAP2K4|Tier1,NCOR1|Tier1,SPECC1|Tier2,NF1|Tier1,SUZ12|Tier1;DisruptL=SMYD4;DisruptR=RASL10B,TAF15;Fusion=SMYD4+RASL10B|SMYD4+TAF15;ClosestL=SERPINF1;ClosestR=GAS2L2	168977	36041470	10,1788505,35740201	0,0,0
chr17	26663483	26663484	chr20	31572794	31572795	TRA	NA	+	+	[Manta_PE=4,Manta_SR=3],[Lumpy_PE=2,Lumpy_SR=2]	manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=HM13,HM13-AS1;ClosestL=;ClosestR=AL110115.2	22044138	31539739	3,26663485,31572795	0,0,0
chr17	34007794	34007795	chr17	34345231	34345232	INV	NA	-	-	[Svaba_SR=33,Svaba_PE=44],[Manta_PE=42,Manta_SR=28],[Lumpy_PE=29,Lumpy_SR=24]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC024610.2,AC004147.4,ASIC2;DisruptR=;ClosestL=AC123769.1;ClosestR=CCL13	34345057	34345058	24,34007794,34345231	0,0,0
chr17	34019945	34019946	chr17	43351893	43351894	DEL	NA	+	-	[Svaba_SR=43,Svaba_PE=48],[Manta_PE=43,Manta_SR=36],[Lumpy_PE=29,Lumpy_SR=28]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=CCR7|Tier2,TAF15|Tier1,MLLT6|Tier1,LASP1|Tier1,CDK12|Tier1,RARA|Tier1,ERBB2|Tier1,SMARCE1|Tier1,STAT5B|Tier1,STAT3|Tier1,BRCA1|Tier1;DisruptL=AC024610.2,AC004147.4,ASIC2;DisruptR=;ClosestL=AC123769.1;ClosestR=AC109326.1	34345057	43301597	27,34019945,43351893	0,0,0
chr17	35981786	35981787	chr17	35985681	35985682	INV	NA	-	-	[Svaba_SR=30,Svaba_PE=27],[Manta_PE=24,Manta_SR=25],[Lumpy_PE=15,Lumpy_SR=15]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CCL14,AC244100.2,CCL15-CCL14;ClosestL=CCL16;ClosestR=CCL16	36041470	36041470	21,35981786,35985676	0,0,0
chr17	36183293	36183294	chr17	36184037	36184038	INV	NA	+	+	[Svaba_SR=39,Svaba_PE=45],[Manta_PE=37,Manta_SR=32],[Lumpy_PE=32,Lumpy_SR=25]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC243829.1;DisruptR=AC243829.1;ClosestL=AC243829.2;ClosestR=AC243829.2	36041471	36041471	15,36183291,36184038	0,0,0
chr17	39577411	39577412	chr17	39805140	39805141	DUP	NA	-	+	[Svaba_SR=41,Svaba_PE=56],[Manta_PE=56,Manta_SR=28],[Lumpy_PE=56,Lumpy_SR=3]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=ERBB2|Tier1;DisruptL=;DisruptR=IKZF3;ClosestL=AC009283.1;ClosestR=	39577425	39805110	28,39577413,39805141	0,0,0
chr17	44549222	44549223	chr17	44628027	44628028	DEL	NA	+	-	[Svaba_SR=42,Svaba_PE=46],[Manta_PE=45,Manta_SR=34],[Lumpy_PE=24,Lumpy_SR=22]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=FZD2;ClosestR=SMCO4P1	43301597	43301597	27,44549223,44628027	0,0,0
chr17	44682949	44682950	chr22	28755129	28755130	TRA	NA	-	+	[Lumpy_PE=2,Lumpy_SR=2]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MEIOC,CCDC43;DisruptR=HSCB;Fusion=HSCB-MEIOC;ClosestL=AC091152.2;ClosestR=CHEK2	43301597	29344638	2,44682947,28755130	0,0,0
chr17	47874904	47874905	chr17	48072313	48072314	DUP	NA	-	+	[Svaba_SR=43,Svaba_PE=127],[Manta_PE=114,Manta_SR=82],[Lumpy_PE=95,Lumpy_SR=39]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CBX1;ClosestL=AC018521.7;ClosestR=AC004477.3	47874813	48072290	2,47874899,48072313	0,0,0
chr17	55526546	55526547	chr17	55537682	55537683	INV	NA	-	-	[Svaba_SR=32,Svaba_PE=20],[Manta_PE=13,Manta_SR=26],[Lumpy_PE=9,Lumpy_SR=21]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=AC105021.1;ClosestL=AC105021.1;ClosestR=GARSP1	55607901	55607901	24,55526545,55537682	0,0,0
chr17	55526721	55526722	chr21	41571013	41571014	TRA	NA	+	-	[Svaba_SR=28,Svaba_PE=27],[Manta_PE=22,Manta_SR=21],[Lumpy_PE=17,Lumpy_SR=17]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC105021.1;ClosestR=AP006748.1	55607901	41825925	20,55526722,41571013	0,0,0
chr17	55527606	55527607	chr17	55538276	55538277	INV	NA	+	+	[Svaba_SR=19,Svaba_PE=15],[Manta_PE=15,Manta_SR=16],[Lumpy_PE=12,Lumpy_SR=14]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC105021.1;DisruptR=AC105021.1;ClosestL=SMIM36;ClosestR=GARSP1	55607901	55607901	14,55527605,55538277	0,0,0
chr17	55537681	55537682	chr21	41571012	41571013	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=20],[Manta_PE=16,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC105021.1;DisruptR=;ClosestL=GARSP1;ClosestR=AP006748.1	55607901	41825925	0,0,0	0,0,0
chr17	55607904	55607905	chr17	59518907	59518908	DUP	NA	-	+	[Svaba_SR=72,Svaba_PE=97],[Manta_PE=78,Manta_SR=62],[Lumpy_PE=71,Lumpy_SR=21]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=RNF43|Tier1,MSI2|Tier1;DisruptL=;DisruptR=LINC01476;ClosestL=;ClosestR=RNU4-13P	55607902	59518847	47,55607906,59518908	0,0,0
chr17	67102576	67102577	chr17	67113691	67113692	INV	NA	-	-	[Svaba_SR=71,Svaba_PE=58],[Manta_PE=62,Manta_SR=59],[Lumpy_PE=43,Lumpy_SR=43]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=HELZ;DisruptR=HELZ;ClosestL=;ClosestR=	67102560	67102560	44,67102576,67113691	0,0,0
chr17	71544176	71544177	chr17	71545941	71545942	DEL	NA	+	-	[Svaba_SR=30,Svaba_PE=30],[Manta_PE=27,Manta_SR=30],[Lumpy_PE=20,Lumpy_SR=13]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	67102560	67102560	0,0,0	0,0,0
chr17	72463523	72463524	chr17	72475017	72475018	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=14],[Manta_PE=14,Manta_SR=19],[Lumpy_PE=10,Lumpy_SR=16]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR=	67102560	67102560	16,72463525,72475016	0,0,0
chr17	72466028	72466029	chr17	72472943	72472944	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=19],[Manta_PE=18,Manta_SR=18],[Lumpy_PE=12,Lumpy_SR=15]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR=	67102560	67102560	19,72466023,72472943	0,0,0
chr17	72474704	72474705	chr17	72485602	72485603	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=29],[Manta_PE=27,Manta_SR=21],[Lumpy_PE=20,Lumpy_SR=15]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR=	67102560	67102560	15,72474708,72485598	0,0,0
chr17	72475233	72475234	chr17	72534012	72534013	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=20],[Manta_PE=18,Manta_SR=16],[Lumpy_PE=9,Lumpy_SR=12]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR=	67102560	67102560	13,72475229,72534012	0,0,0
chr17	72487296	72487297	chrX	116501145	116501146	TRA	NA	+	+	[Svaba_SR=49,Svaba_PE=20],[Manta_PE=13,Manta_SR=0]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC00511;DisruptR=;ClosestL=;ClosestR=	67102560	116456071	0,0,0	0,0,0
chr17	72487296	72487297	chrX	76243013	76243014	TRA	NA	+	+	[Svaba_SR=28,Svaba_PE=14],[Manta_PE=16,Manta_SR=23],[Lumpy_PE=12,Lumpy_SR=16]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=LINC00511;DisruptR=;ClosestL=;ClosestR=RNU6-867P	67102560	76245723	21,72487298,76243018	0,0,0
chr17	77464133	77464134	chr17	77464639	77464640	DEL	NA	+	-	[Svaba_SR=4,Svaba_PE=0]	svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=SEPT9|Tier2;DisruptL=SEPT9;DisruptR=SEPT9;ClosestL=AC111170.2;ClosestR=AC111170.2	83247341	83247341	0,0,0	0,0,0
chr17	81921915	81921916	chr21	14696103	14696104	TRA	NA	-	-	[Manta_PE=30,Manta_SR=47]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MAFG;DisruptR=;ClosestL=SIRT7;ClosestR=	83247341	15873584	35,81921917,14696100	0,0,0
chr17	81922131	81922132	chr21	14696028	14696029	TRA	NA	+	-	[Svaba_SR=45,Svaba_PE=31],[Manta_PE=5,Manta_SR=39],[Lumpy_PE=29,Lumpy_SR=27]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MAFG;DisruptR=;ClosestL=AC145207.8;ClosestR=	83247341	15873584	18,81922133,14696028	0,0,0
chr17	81922131	81922132	chr21	14696627	14696628	TRA	NA	+	-	[Svaba_SR=68,Svaba_PE=0],[Manta_PE=29,Manta_SR=40]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MAFG;DisruptR=;ClosestL=AC145207.8;ClosestR=	83247341	15873584	0,0,0	0,0,0
chr17	81996893	81996894	chr17	81997849	81997850	DEL	NA	+	-	[Svaba_SR=2,Svaba_PE=5],[Lumpy_PE=3,Lumpy_SR=2]	lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=ASPSCR1|Tier1;DisruptL=ASPSCR1;DisruptR=ASPSCR1;ClosestL=;ClosestR=	83247341	83247341	3,81996896,81997852	0,0,0
chr18	1091199	1091200	chr18	1158740	1158741	DEL	NA	+	-	[Svaba_SR=76,Svaba_PE=105],[Manta_PE=97,Manta_SR=62],[Lumpy_PE=76,Lumpy_SR=23]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AP005328.1;DisruptR=AP005328.1;ClosestL=;ClosestR=AP005265.1	1091193	1158564	47,1091196,1158740	0,0,0
chr18	1442130	1442131	chr18	1517728	1517729	DEL	NA	+	-	[Manta_PE=8,Manta_SR=8]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=AC008109.1;ClosestL=;ClosestR=	1158564	1158564	10,1442132,1517729	0,0,0
chr18	1792586	1792587	chr18	30132066	30132067	DUP	NA	-	+	[Svaba_SR=4,Svaba_PE=7],[Manta_PE=5,Manta_SR=3],[Lumpy_PE=5,Lumpy_SR=3]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=SS18|Tier1,ZNF521|Tier1;DisruptL=;DisruptR=;ClosestL=AP005057.1;ClosestR=	1158564	30129851	3,1792587,30132067	0,0,0
chr18	2056157	2056158	chr18	2057225	2057226	INV	NA	+	+	[Svaba_SR=4,Svaba_PE=5],[Lumpy_PE=6,Lumpy_SR=3]	svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AP005230.1;DisruptR=AP005230.1;ClosestL=;ClosestR=	1158564	1158564	4,2056154,2057226	0,0,0
chr18	5693420	5693421	chr18	10125703	10125704	DUP	NA	-	+	[Svaba_SR=23,Svaba_PE=20],[Manta_PE=19,Manta_SR=22],[Lumpy_PE=17,Lumpy_SR=7]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=AP005271.1;ClosestL=;ClosestR=	7909753	11293417	21,5693420,10125704	0,0,0
chr18	8331815	8331816	chr18	8670390	8670391	INV	NA	-	-	[Svaba_SR=20,Svaba_PE=19],[Manta_PE=20,Manta_SR=18],[Lumpy_PE=16,Lumpy_SR=10]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PTPRM;DisruptR=;ClosestL=;ClosestR=TOMM20P3	7909754	7909754	13,8331814,8670390	0,0,0
chr18	9792146	9792147	chr18	9856621	9856622	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=15],[Manta_PE=17,Manta_SR=19],[Lumpy_PE=12,Lumpy_SR=15]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RAB31;DisruptR=RAB31;ClosestL=ZNF415P1;ClosestR=RNA5SP449	11293417	11293417	17,9792147,9856621	0,0,0
chr18	11707495	11707496	chr21	9022992	9022993	TRA	NA	+	-	[Svaba_SR=38,Svaba_PE=63],[Manta_PE=48,Manta_SR=55]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=GNAL;DisruptR=;ClosestL=;ClosestR=CR392039.2	11707458	13282812	34,11707494,9022992	0,0,0
chr18	14810726	14810727	chr18	14817612	14817613	DEL	NA	+	-	[Svaba_SR=16,Svaba_PE=25],[Manta_PE=19,Manta_SR=13],[Lumpy_PE=18,Lumpy_SR=1]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ANKRD30B;DisruptR=AP006565.1,ANKRD30B;ClosestL=AP006565.1;ClosestR=MIR3156-2	11707458	11707458	12,14810731,14817612	0,0,0
chr18	23307636	23307637	chr20	31539702	31539703	TRA	NA	-	-	[Svaba_SR=96,Svaba_PE=114],[Manta_PE=104,Manta_SR=83],[Lumpy_PE=74,Lumpy_SR=48]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=TMEM241;DisruptR=HM13;Fusion=TMEM241-HM13;ClosestL=;ClosestR=AL110115.1	23307596	31539738	52,23307637,31539702	0,0,0
chr18	24278556	24278557	chr18	24279392	24279393	INV	NA	+	+	[Svaba_SR=20,Svaba_PE=22],[Manta_PE=20,Manta_SR=17],[Lumpy_PE=16,Lumpy_SR=14]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=OSBPL1A;DisruptR=OSBPL1A;ClosestL=;ClosestR=	24279287	24279288	13,24278557,24279393	0,0,0
chr18	59214242	59214243	chr18	59217204	59217205	DUP	NA	-	+	[Svaba_SR=26,Svaba_PE=26],[Manta_PE=25,Manta_SR=25],[Lumpy_PE=20,Lumpy_SR=20]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=GRP;ClosestR=GRP	59280927	59280927	23,59214241,59217205	0,0,0
chr18	59281023	59281024	chr18	60359158	60359159	DEL	NA	+	-	[Svaba_SR=14,Svaba_PE=14],[Manta_PE=16,Manta_SR=13],[Lumpy_PE=12,Lumpy_SR=11]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CPLX4;DisruptR=;ClosestL=RAX;ClosestR=MC4R	59280928	59280928	12,59281019,60359158	0,0,0
chr19	8257771	8257772	chr22	24989957	24989958	TRA	NA	-	-	[Svaba_SR=7,Svaba_PE=3],[Manta_PE=4,Manta_SR=6],[Lumpy_PE=2,Lumpy_SR=4]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CERS4;DisruptR=KIAA1671;ClosestL=AC022146.2;ClosestR=AL022323.3	12858860	24015969	6,8257772,24989957	0,0,0
chr19	8258007	8258008	chr22	24987321	24987322	TRA	NA	+	-	[Svaba_SR=4,Svaba_PE=4],[Manta_PE=5,Manta_SR=4],[Lumpy_PE=3,Lumpy_SR=1]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CERS4;DisruptR=KIAA1671;Fusion=CERS4-KIAA1671;ClosestL=AC022146.2;ClosestR=	12858860	24015969	3,8258009,24987321	0,0,0
chr19	12858913	12858914	chr19	12880038	12880039	DEL	NA	+	-	[Svaba_SR=55,Svaba_PE=63],[Manta_PE=48,Manta_SR=49],[Lumpy_PE=33,Lumpy_SR=41]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=HOOK2,MAST1;DisruptR=DNASE2;Fusion=DNASE2+HOOK2;ClosestL=MIR6794;ClosestR=AC020934.2	12858861	12880013	29,12858913,12880038	0,0,0
chr19	14687538	14687539	chr19	14928275	14928276	INV	NA	-	-	[Svaba_SR=78,Svaba_PE=59],[Manta_PE=46,Manta_SR=72]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ADGRE3;DisruptR=;ClosestL=ZNF333;ClosestR=OR7A15P	14687524	14687524	10,14687533,14928269	0,0,0
chr19	14707786	14707787	chr19	14913582	14913583	DUP	NA	-	+	[Svaba_SR=107,Svaba_PE=84],[Manta_PE=105,Manta_SR=82],[Lumpy_PE=105,Lumpy_SR=9]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ZNF333;DisruptR=;ClosestL=ADGRE3;ClosestR=OR7A11P	14687524	14687524	0,0,0	0,0,0
chr19	14928300	14928301	chr19	15379943	15379944	INV	NA	-	-	[Svaba_SR=34,Svaba_PE=42],[Manta_PE=44,Manta_SR=31],[Lumpy_PE=35,Lumpy_SR=11]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=BRD4|Tier1;DisruptL=;DisruptR=AC005785.1;ClosestL=OR7A15P;ClosestR=AKAP8L	14687524	15684658	20,14928302,15379943	0,0,0
chr19	15195290	15195291	chr19	15634158	15634159	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=12],[Manta_PE=11,Manta_SR=10],[Lumpy_PE=11,Lumpy_SR=10]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=BRD4|Tier1;DisruptL=NOTCH3;DisruptR=;ClosestL=MIR6795;ClosestR=CYP4F8	15684658	15684658	0,0,0	0,0,0
chr19	15217850	15217851	chr19	15218433	15218434	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AC004257.1;ClosestR=AC004257.1	15684658	15684658	0,0,0	0,0,0
chr19	15329197	15329198	chr19	20490430	20490431	INV	NA	+	+	[Svaba_SR=39,Svaba_PE=42],[Manta_PE=42,Manta_SR=34],[Lumpy_PE=39,Lumpy_SR=13]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=TPM4|Tier1,JAK3|Tier1,ELL|Tier1,CRTC1|Tier1;DisruptL=BRD4;DisruptR=AC008554.1;Fusion=AC008554.1+BRD4;ClosestL=AC005776.1;ClosestR=	15684658	20490395	25,15329201,20490431	0,0,0
chr19	15384118	15384119	chr19	15506506	15506507	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=22],[Manta_PE=19,Manta_SR=15],[Lumpy_PE=14,Lumpy_SR=8]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AKAP8L;DisruptR=;ClosestL=AC005785.2;ClosestR=CYP4F22	15684658	15684658	13,15384120,15506506	0,0,0
chr19	15523081	15523082	chr19	15546350	15546351	INV	NA	-	-	[Svaba_SR=87,Svaba_PE=65],[Manta_PE=59,Manta_SR=71],[Lumpy_PE=58,Lumpy_SR=1]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CYP4F22;DisruptR=CYP4F22;ClosestL=AC011492.1;ClosestR=CYP4F23P	15684658	15684658	56,15523081,15546350	0,0,0
chr19	15533868	15533869	chr19	15684645	15684646	INV	NA	+	+	[Svaba_SR=178,Svaba_PE=88],[Manta_PE=194,Manta_SR=169]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CYP4F22;DisruptR=CYP4F12;ClosestL=AC011492.1;ClosestR=CYP4F10P	15684658	15684658	77,15533870,15684646	0,0,0
chr19	15588870	15588871	chr19	15589780	15589781	DEL	NA	+	-	[Svaba_SR=97,Svaba_PE=151],[Manta_PE=126,Manta_SR=115],[Lumpy_PE=136,Lumpy_SR=91]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=CYP4F23P;ClosestR=CYP4F23P	15684658	15684658	69,15588872,15589780	0,0,0
chr19	15632140	15632141	chr19	20137691	20137692	DEL	NA	+	-	[Svaba_SR=71,Svaba_PE=65],[Manta_PE=63,Manta_SR=48],[Lumpy_PE=61,Lumpy_SR=3]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=TPM4|Tier1,JAK3|Tier1,ELL|Tier1,CRTC1|Tier1;DisruptL=;DisruptR=AC011447.2,AC011447.3;ClosestL=CYP4F8;ClosestR=BNIP3P15	15684658	20137238	41,15632139,20137687	0,0,0
chr19	17316666	17316667	chr19	17362636	17362637	DEL	NA	+	-	[Svaba_SR=6,Svaba_PE=14],[Manta_PE=14,Manta_SR=5],[Lumpy_PE=13,Lumpy_SR=2]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=DDA1;DisruptR=AC010463.2,PLVAP;Fusion=DDA1+AC010463.2;ClosestL=ABHD8;ClosestR=GTPBP3	15684659	15684659	4,17316668,17362635	0,0,0
chr19	20300586	20300587	chr19	20303756	20303757	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=33],[Manta_PE=31,Manta_SR=15],[Lumpy_PE=21,Lumpy_SR=10]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC078899.4,AC011447.3;DisruptR=AC078899.4,AC011447.3;ClosestL=;ClosestR=	20137238	20137238	12,20300585,20303756	0,0,0
chr19	20441327	20441328	chr19	20443259	20443260	DEL	NA	+	-	[Svaba_SR=67,Svaba_PE=85],[Manta_PE=73,Manta_SR=51],[Lumpy_PE=57,Lumpy_SR=7]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC008554.1;DisruptR=BNIP3P23,AC008554.1;ClosestL=BNIP3P23;ClosestR=ZNF826P	20490394	20490394	44,20441329,20443255	0,0,0
chr19	20497266	20497267	chr19	20498447	20498448	INV	NA	+	+	[Svaba_SR=23,Svaba_PE=25],[Manta_PE=26,Manta_SR=20],[Lumpy_PE=17,Lumpy_SR=15]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR=	20490395	20490395	16,20497268,20498448	0,0,0
chr19	20497437	20497438	chr19	20501960	20501961	DUP	NA	-	+	[Svaba_SR=33,Svaba_PE=36],[Manta_PE=31,Manta_SR=34],[Lumpy_PE=29,Lumpy_SR=13]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR=	20490395	20490395	28,20497438,20501961	0,0,0
chr19	20498993	20498994	chr19	20507532	20507533	DUP	NA	-	+	[Svaba_SR=28,Svaba_PE=0],[Manta_PE=33,Manta_SR=27],[Lumpy_PE=28,Lumpy_SR=24]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR=	20490395	20490395	23,20498993,20507533	0,0,0
chr19	20506933	20506934	chr19	24352249	24352250	DUP	NA	-	+	[Svaba_SR=36,Svaba_PE=29],[Manta_PE=33,Manta_SR=32],[Lumpy_PE=22,Lumpy_SR=10]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=ZNF429|Tier2;DisruptL=AC008554.1;DisruptR=;ClosestL=;ClosestR=	20490395	24018596	14,20506933,24352271	0,0,0
chr19	23544106	23544107	chr19	23692932	23692933	INV	NA	-	-	[Manta_PE=4,Manta_SR=10]	manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ZNF675;DisruptR=;ClosestL=;ClosestR=ZNF675	23544109	23544110	0,0,0	0,0,0
chr19	24348141	24348142	chr19	24353031	24353032	INV	NA	-	-	[Svaba_SR=37,Svaba_PE=31],[Manta_PE=31,Manta_SR=31],[Lumpy_PE=19,Lumpy_SR=22]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	24018596	24018596	25,24348141,24353031	0,0,0
chr19	24373673	24373674	chr19	24375338	24375339	DEL	NA	+	-	[Svaba_SR=25,Svaba_PE=29],[Manta_PE=32,Manta_SR=30]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	24018596	24018596	19,24373656,24375338	0,0,0
chr20	14979687	14979688	chr20	15067580	15067581	DEL	NA	+	-	[Svaba_SR=12,Svaba_PE=4]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MACROD2;DisruptR=MACROD2;ClosestL=;ClosestR=	8764420	8764420	0,0,0	0,0,0
chr20	15067580	15067581	chr20	15078347	15078348	DUP	NA	-	+	[Svaba_SR=8,Svaba_PE=5],[Manta_PE=5,Manta_SR=7],[Lumpy_PE=3,Lumpy_SR=2]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MACROD2;DisruptR=MACROD2;ClosestL=;ClosestR=	8764420	8764420	3,15067585,15078348	0,0,0
chr20	18763090	18763091	chr20	18763944	18763945	INV	NA	-	-	[Svaba_SR=3,Svaba_PE=8],[Lumpy_PE=5,Lumpy_SR=3]	lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=DTD1;DisruptR=DTD1;ClosestL=AL121900.2;ClosestR=EEF1A1P34	21885644	21885644	3,18763090,18763944	0,0,0
chr20	22251586	22251587	chr20	22253038	22253039	INV	NA	-	-	[Svaba_SR=0,Svaba_PE=10],[Manta_PE=13,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=LINC01427;ClosestR=LINC01427	21885645	21885645	0,0,0	0,0,0
chr20	26330213	26330214	chr20	26331691	26331692	DEL	NA	+	-	[Svaba_SR=11,Svaba_PE=23],[Manta_PE=23,Manta_SR=12]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	28506070	28506070	4,26330156,26331691	0,0,0
chr20	31074163	31074164	chr20	34232004	34232005	DUP	NA	-	+	[Svaba_SR=51,Svaba_PE=55]	svaba	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=ASXL1|Tier1;DisruptL=;DisruptR=ASIP;ClosestL=;ClosestR=AL035458.2	31245066	34230621	35,31074151,34232005	0,0,0
chr20	31360012	31360013	chr20	31377616	31377617	DUP	NA	-	+	[Lumpy_PE=3,Lumpy_SR=2]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=DEFB119;ClosestL=DEFB117;ClosestR=RF00561	31245066	31245066	4,31360011,31377616	0,0,0
chr20	33809332	33809333	chr20	33809994	33809995	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ZNF341-AS1;DisruptR=ZNF341-AS1;ClosestL=CHMP4B;ClosestR=CHMP4B	34230620	34230620	0,0,0	0,0,0
chr20	36914523	36914524	chr20	36933537	36933538	INV	NA	+	+	[Svaba_SR=15,Svaba_PE=22],[Manta_PE=26,Manta_SR=12],[Lumpy_PE=24,Lumpy_SR=5]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SAMHD1;DisruptR=SAMHD1;ClosestL=;ClosestR=	36912831	36912831	11,36914523,36933538	0,0,0
chr20	47103302	47103303	chr20	47104389	47104390	DEL	NA	+	-	[Svaba_SR=29,Svaba_PE=19],[Manta_PE=17,Manta_SR=18]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=EYA2;DisruptR=EYA2;ClosestL=;ClosestR=	39349551	39349551	0,0,0	0,0,0
chr20	47104471	47104472	chr20	47225242	47225243	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=8],[Lumpy_PE=3,Lumpy_SR=2]	lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=EYA2;DisruptR=ZMYND8;ClosestL=;ClosestR=	39349551	39349551	3,47104393,47225243	0,0,0
chr20	47225235	47225236	chr20	47268863	47268864	DEL	NA	+	-	[Svaba_SR=42,Svaba_PE=13],[Manta_PE=10,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ZMYND8;DisruptR=ZMYND8;ClosestL=;ClosestR=	39349551	39349551	0,0,0	0,0,0
chr20	48179659	48179660	chr20	48180192	48180193	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=0],[Manta_PE=18,Manta_SR=19],[Lumpy_PE=11,Lumpy_SR=16]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=;ClosestR=	39349551	39349551	19,48179660,48180192	0,0,0
chr21	9888809	9888810	chr21	21141002	21141003	DEL	NA	+	-	[Svaba_SR=16,Svaba_PE=17]	svaba	HCC-1143_80--HCC-1143BL_40	known=;gap;DisruptL=;DisruptR=NCAM2;ClosestL=RN7SL52P;ClosestR=	13282812	20111384	10,9888810,21141002	0,0,0
chr21	10328063	10328064	chr21	10333401	10333402	DUP	NA	-	+	[Svaba_SR=20,Svaba_PE=13]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=AP003900.1;ClosestL=AP003900.1;ClosestR=EIF3FP1	13282812	13282812	12,10328062,10333402	0,0,0
chr21	10570015	10570016	chr21	20715590	20715591	INV	NA	+	+	[Svaba_SR=10,Svaba_PE=2]	svaba	HCC-1143_80--HCC-1143BL_40	known=;gap;DisruptL=TPTE,AF254983.1;DisruptR=;ClosestL=CYCSP41;ClosestR=	13282812	20111384	0,0,0	0,0,0
chr21	13283045	13283046	chr21	13506275	13506276	DEL	NA	+	-	[Svaba_SR=42,Svaba_PE=52],[Manta_PE=48,Manta_SR=44]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=GTF2IP2	13282812	13507200	36,13283046,13506275	0,0,0
chr21	15873590	15873591	chr21	16679496	16679497	INV	NA	+	+	[Svaba_SR=126,Svaba_PE=125],[Manta_PE=135,Manta_SR=105],[Lumpy_PE=104,Lumpy_SR=83]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=USP25;DisruptR=;ClosestL=;ClosestR=	15873585	17474345	65,15873592,16679497	0,0,0
chr21	16672953	16672954	chr21	17986177	17986178	DUP	NA	-	+	[Svaba_SR=117,Svaba_PE=127],[Manta_PE=105,Manta_SR=93],[Lumpy_PE=85,Lumpy_SR=76]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=CHODL;ClosestL=;ClosestR=	15873585	17986205	64,16672958,17986178	0,0,0
chr21	17474427	17474428	chr21	41078325	41078326	DUP	NA	-	+	[Svaba_SR=124,Svaba_PE=153],[Manta_PE=131,Manta_SR=116],[Lumpy_PE=109,Lumpy_SR=87]	manta,lumpy,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=OLIG2|Tier1,RUNX1|Tier1,ERG|Tier1;DisruptL=;DisruptR=;ClosestL=;ClosestR=	17474346	41078299	70,17474426,41078326	0,0,0
chr21	17592650	17592651	chr21	17621842	17621843	DUP	NA	-	+	[Svaba_SR=20,Svaba_PE=30],[Manta_PE=29,Manta_SR=15],[Lumpy_PE=27,Lumpy_SR=11]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=CXADR;DisruptR=BTG3-AS1;Fusion=BTG3-AS1+CXADR;ClosestL=BTG3;ClosestR=BTG3	17474346	17474346	13,17592651,17621843	0,0,0
chr21	25706466	25706467	chr21	25706995	25706996	DEL	NA	+	-	[Svaba_SR=4,Svaba_PE=0]	svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=JAM2;DisruptR=JAM2;ClosestL=ATP5PF;ClosestR=ATP5PF	26635290	26635290	0,0,0	0,0,0
chr21	31947365	31947366	chr21	45927270	45927271	INV	NA	-	-	[Svaba_SR=0,Svaba_PE=68],[Manta_PE=61,Manta_SR=0]	manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=OLIG2|Tier1,TMPRSS2|Tier1,U2AF1|Tier1,RUNX1|Tier1,ERG|Tier1;DisruptL=HUNK;DisruptR=PCBP3;ClosestL=;ClosestR=AJ239328.1	31947285	46107841	2,31947365,45927258	0,0,0
chr21	34819613	34819614	chr21	34850895	34850896	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=27],[Manta_PE=26,Manta_SR=16],[Lumpy_PE=20,Lumpy_SR=14]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=RUNX1|Tier1;DisruptL=RUNX1;DisruptR=RUNX1;ClosestL=;ClosestR=	34819639	34847755	13,34819611,34850895	0,0,0
chr21	40764330	40764331	chr21	44064618	44064619	INV	NA	-	-	[Svaba_SR=111,Svaba_PE=133],[Manta_PE=145,Manta_SR=106],[Lumpy_PE=103,Lumpy_SR=56]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=TMPRSS2|Tier1,U2AF1|Tier1;DisruptL=DSCAM;DisruptR=TRAPPC10;Fusion=DSCAM+TRAPPC10;ClosestL=;ClosestR=H2AFZP1	40764260	44064550	5,40764317,44064618	0,0,0
chr21	41822940	41822941	chr21	42103805	42103806	DUP	NA	-	+	[Svaba_SR=42,Svaba_PE=94],[Manta_PE=79,Manta_SR=62],[Lumpy_PE=73,Lumpy_SR=43]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PRDM15;DisruptR=UMODL1-AS1,UMODL1;Fusion=PRDM15+UMODL1-AS1;ClosestL=;ClosestR=	41825925	42103908	39,41822941,42103806	0,0,0
chr21	41823975	41823976	chr21	46107855	46107856	INV	NA	+	+	[Svaba_SR=78,Svaba_PE=89],[Manta_PE=102,Manta_SR=75],[Lumpy_PE=90,Lumpy_SR=39]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=U2AF1|Tier1;DisruptL=PRDM15;DisruptR=COL6A2;Fusion=COL6A2+PRDM15;ClosestL=;ClosestR=AP001471.1	41825925	46107842	49,41823975,46107856	0,0,0
chr21	41825929	41825930	chr21	45927312	45927313	DUP	NA	-	+	[Svaba_SR=30,Svaba_PE=133],[Manta_PE=139,Manta_SR=60],[Lumpy_PE=136,Lumpy_SR=36]	manta,svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=U2AF1|Tier1;DisruptL=PRDM15;DisruptR=PCBP3;ClosestL=;ClosestR=AJ239328.1	41825926	46107841	30,41825930,45927313	0,0,0
chr21	41831216	41831217	chr21	41833962	41833963	DEL	NA	+	-	[Svaba_SR=109,Svaba_PE=140],[Manta_PE=119,Manta_SR=91],[Lumpy_PE=94,Lumpy_SR=65]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=PRDM15;DisruptR=PRDM15;ClosestL=;ClosestR=	41825926	41825926	59,41831218,41833962	0,0,0
chr21	42948646	42948647	chr21	42950135	42950136	DEL	NA	+	-	[Svaba_SR=68,Svaba_PE=53],[Manta_PE=62,Manta_SR=60],[Lumpy_PE=43,Lumpy_SR=25]	svaba,manta,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=MIR5692B;ClosestR=MIR5692B	42103909	42103909	39,42948644,42950135	0,0,0
chr22	16812440	16812441	chr22	27132898	27132899	INV	NA	-	-	[Manta_PE=3,Manta_SR=6],[Lumpy_PE=2,Lumpy_SR=4]	lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;gap;Cancer_census=SEPT5|Tier2,DGCR8|Tier2,LZTR1|Tier1,MAPK1|Tier1,SMARCB1|Tier1,CLTCL1|Tier1,BCR|Tier1;DisruptL=XKR3;DisruptR=;ClosestL=HSFY1P1;ClosestR=AL008638.1	10514978	29344638	6,16812445,27132894	0,0,0
chr22	20476966	20476967	chr22	20591962	20591963	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=25],[Manta_PE=23,Manta_SR=15],[Lumpy_PE=16,Lumpy_SR=12]	svaba,lumpy,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=KLHL22;DisruptR=CCDC74BP1;Fusion=CCDC74BP1+KLHL22;ClosestL=RNY1P9;ClosestR=MED15	24015968	24015968	12,20476962,20591962	0,0,0
chr22	23936453	23936454	chr22	23946301	23946302	INV	NA	-	-	[Svaba_SR=24,Svaba_PE=21],[Manta_PE=9,Manta_SR=22]	svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;ClosestL=AP000350.1;ClosestR=AP000350.1	24015968	24015968	18,23936454,23946301	0,0,0
chr22	23943022	23943023	chr22	23949661	23949662	DEL	NA	+	-	[Svaba_SR=16,Svaba_PE=15]	svaba	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=AP000350.1;ClosestR=AP000350.3	24015968	24015968	8,23943023,23949661	0,0,0
chr22	25536845	25536846	chr22	25555999	25556000	DEL	NA	+	-	[Svaba_SR=4,Svaba_PE=2],[Lumpy_PE=3,Lumpy_SR=2]	svaba,lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=CRYBB2P1;ClosestR=AL022329.1	24015969	24015969	3,25536846,25555999	0,0,0
chr22	25537886	25537887	chr22	25554449	25554450	DUP	NA	-	+	[Lumpy_PE=4,Lumpy_SR=1]	lumpy	HCC-1143_80--HCC-1143BL_40	known=;ClosestL=CRYBB2P1;ClosestR=AL022329.1	24015969	24015969	0,0,0	0,0,0
chr22	29187777	29187778	chr22	29344659	29344660	DUP	NA	-	+	[Svaba_SR=38,Svaba_PE=49],[Manta_PE=44,Manta_SR=39],[Lumpy_PE=37,Lumpy_SR=17]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=EWSR1|Tier1;DisruptL=;DisruptR=AP1B1;ClosestL=RNU6-1219P;ClosestR=MIR3653	29344638	29344639	27,29187768,29344660	0,0,0
chr22	29285161	29285162	chr22	29286804	29286805	INV	NA	+	+	[Svaba_SR=15,Svaba_PE=26],[Manta_PE=25,Manta_SR=18],[Lumpy_PE=23,Lumpy_SR=5]	lumpy,manta,svaba	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=EWSR1|Tier1;DisruptL=EWSR1;DisruptR=EWSR1;ClosestL=RHBDD3;ClosestR=RHBDD3	29344638	29344638	8,29285160,29286805	0,0,0
chr22	46073953	46073954	chr22	46234169	46234170	DUP	NA	-	+	[Svaba_SR=68,Svaba_PE=62],[Manta_PE=52,Manta_SR=57],[Lumpy_PE=45,Lumpy_SR=52]	lumpy,svaba,manta	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=MIRLET7BHG;DisruptR=PPARA;Fusion=PPARA+MIRLET7BHG;ClosestL=AL121672.2;ClosestR=CDPF1	46073919	46234134	44,46073952,46234170	0,0,0