#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=24,Svaba_PE=31],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=24,Lumpy_SR=11]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=ARAF|Tier2,KDM6A|Tier1,RBM10|Tier1;DisruptL=KDM6A;DisruptR=UXT;ClosestL=;ClosestR=UXT-AS1	44887175	47658809	16,44887191,47658827	0,0,0
chrX	45136456	45136457	chrX	45137951	45137952	DEL	NA	+	-	[Svaba_SR=40,Svaba_PE=39],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=26,Lumpy_SR=15]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=CXorf36;ClosestR=CXorf36	44887175	44887175	24,45136456,45137950	0,0,0
chrX	57361939	57361940	chrX	57364610	57364611	INV	NA	-	-	[Svaba_SR=18,Svaba_PE=15],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=10,Lumpy_SR=14]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=FAAH2;DisruptR=FAAH2;ClosestL=;ClosestR=	57362136	57362137	15,57361930,57364609	0,0,0
chrX	76242860	76242861	chrX	116501145	116501146	DUP	NA	-	+	[Svaba_SR=24,Svaba_PE=19],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=16]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;Cancer_census=IRS4|Tier1,BTK|Tier1,ATRX|Tier1;DisruptL=;DisruptR=;ClosestL=RNU6-867P;ClosestR=	76241262	115889294	17,76242855,116501150	0,0,0
chrX	76242860	76242861	chrX	76244485	76244486	INV	NA	-	-	[Svaba_SR=29,Svaba_PE=6]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=RNU6-867P;ClosestR=RNU6-867P	76241262	76241262	0,0,0	0,0,0
chrX	76244485	76244486	chrX	116500843	116500844	INV	NA	-	-	[Svaba_SR=17,Svaba_PE=19],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=13,Lumpy_SR=4]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;Cancer_census=IRS4|Tier1,BTK|Tier1,ATRX|Tier1;DisruptL=;DisruptR=;ClosestL=RNU6-867P;ClosestR=	76241262	115889294	12,76244484,116500842	0,0,0
chrX	77209157	77209158	chrX	77304273	77304274	DUP	NA	-	+	[Lumpy_PE=3,Lumpy_SR=2]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	76241262	76241262	2,77209158,77304274	0,0,0
chrX	79973209	79973210	chrX	79982346	79982347	DEL	NA	+	-	[Svaba_SR=27,Svaba_PE=20],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=12,Lumpy_SR=5]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	76241262	76241262	0,0,0	0,0,0
chrX	80459951	80459952	chrX	80462152	80462153	DEL	NA	+	-	[Svaba_SR=54,Svaba_PE=80],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=52,Lumpy_SR=37]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=TENT5D;ClosestR=TENT5D	84382245	84382245	36,80459950,80462151	0,0,0
chrX	84276246	84276247	chrX	84287224	84287225	INV	NA	-	-	[Svaba_SR=18,Svaba_PE=0],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	84382245	84382245	0,0,0	0,0,0
chrX	84380638	84380639	chrX	84382004	84382005	INV	NA	+	+	[Svaba_SR=22,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=21,Lumpy_SR=15]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HDX;DisruptR=HDX;ClosestL=;ClosestR=	84382245	84382245	18,84380640,84382007	0,0,0
chrX	89287531	89287532	chrX	89298078	89298079	DUP	NA	-	+	[Svaba_SR=29,Svaba_PE=12]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	88322773	88322773	20,89287531,89298080	0,0,0
chrX	89754735	89754736	chrX	89755514	89755515	DEL	NA	+	-	[Svaba_SR=8,Svaba_PE=5],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=3]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	88322773	88322773	6,89754737,89755513	0,0,0
chrX	91727150	91727151	chrX	91796419	91796420	DUP	NA	-	+	[Svaba_SR=41,Svaba_PE=29],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=27]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=PCDH11X;ClosestL=;ClosestR=RNU2-26P	88322773	88322773	30,91727141,91796421	0,0,0
chrX	100877602	100877603	chrX	153586485	153586486	INV	NA	+	+	[Svaba_SR=52,Svaba_PE=58],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=42,Lumpy_SR=42]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	41,100877602,153586487	0,0,0
chrX	117971506	117971507	chrX	118882097	118882098	DUP	NA	-	+	[Svaba_SR=56,Svaba_PE=62],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=47,Lumpy_SR=35]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=KLHL13;DisruptR=LINC01285;ClosestL=;ClosestR=AC006965.1	117971510	118882103	34,117971503,118882108	0,0,0
chrX	139747040	139747041	chrX	153271819	153271820	INV	NA	+	+	[Svaba_SR=65,Svaba_PE=47],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;DisruptL=ATP11C;DisruptR=;ClosestL=;ClosestR=AC236972.4	139747068	153149106	47,139747040,153271821	0,0,0
chr1	6465293	6465294	chr3	85183519	85183520	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TNFRSF25;DisruptR=CADM2;ClosestL=PLEKHG5;ClosestR=	6465257	85183522	0,0,0	0,0,0
chr1	6465318	6465319	chr3	85187355	85187356	TRA	NA	+	+	[Svaba_SR=49,Svaba_PE=42],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=24,Lumpy_SR=30]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TNFRSF25;DisruptR=CADM2;Fusion=CADM2-TNFRSF25;ClosestL=PLEKHG5;ClosestR=	6465257	85183523	35,6465320,85187357	0,0,0
chr1	6509232	6509233	chr21	34847762	34847763	TRA	NA	-	-	[Svaba_SR=47,Svaba_PE=21],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=RUNX1|Tier1;DisruptL=PLEKHG5;DisruptR=RUNX1;ClosestL=NOL9;ClosestR=	6465257	34847755	0,0,0	0,0,0
chr1	6509313	6509314	chr1	6510620	6510621	INV	NA	-	-	[Svaba_SR=0,Svaba_PE=13],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=6,Lumpy_SR=15]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PLEKHG5;DisruptR=PLEKHG5;ClosestL=NOL9;ClosestR=NOL9	6465257	6465257	9,6509237,6510620	0,0,0
chr1	6510725	6510726	chr21	34847762	34847763	TRA	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=RUNX1|Tier1;DisruptL=PLEKHG5;DisruptR=RUNX1;Fusion=RUNX1-PLEKHG5;ClosestL=NOL9;ClosestR=	6465257	34847755	19,6510727,34847761	0,0,0
chr1	6623384	6623385	chr1	227866329	227866330	INV	NA	-	-	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=2,Lumpy_SR=33]	lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	223431563	32,6623385,227866328	0,0,0
chr1	6623385	6623386	chr1	227866441	227866442	INV	NA	+	+	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=34]	manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	223431563	28,6623387,227866443	0,0,0
chr1	8115746	8115747	chr1	8341045	8341046	INV	NA	-	-	[Svaba_SR=26,Svaba_PE=23],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=16,Lumpy_SR=16]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AL034417.2;DisruptR=SLC45A1;ClosestL=;ClosestR=RERE	8673895	8673895	21,8115746,8341044	0,0,0
chr1	8337686	8337687	chr1	8341281	8341282	INV	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SLC45A1;DisruptR=SLC45A1;ClosestL=RF00019;ClosestR=RERE	8673895	8673895	15,8337688,8341283	0,0,0
chr1	8673961	8673962	chr1	8950735	8950736	DUP	NA	-	+	[Svaba_SR=49,Svaba_PE=52],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=33,Lumpy_SR=37]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=RERE;DisruptR=CA6;ClosestL=;ClosestR=	8673896	8950766	38,8673963,8950737	0,0,0
chr1	19771904	19771905	chr1	23063404	23063405	DUP	NA	-	+	[Svaba_SR=15,Svaba_PE=12],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=6]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TMCO4;DisruptR=KDM1A,AL031428.1;Fusion=TMCO4+AL031428.1;ClosestL=;ClosestR=MIR4419A	19771881	23062691	13,19771904,23063410	0,0,0
chr1	29400010	29400011	chr6	29804343	29804344	TRA	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=RPL7AP7	23062691	32487100	2,29399832,29804280	0,0,0
chr1	40528747	40528748	chr16	187562	187563	TRA	NA	-	-	[Svaba_SR=22,Svaba_PE=9],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=11]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=ZNF684;ClosestR=Z69706.1	47818751	10005	16,40528747,187559	0,0,0
chr1	40529024	40529025	chrY	56870831	56870832	TRA	NA	+	-	[Svaba_SR=20,Svaba_PE=19]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=ZNF684;ClosestR=CTBP2P1	47818751	-1	19,40529026,56870830	0,0,0
chr1	47818840	47818841	chr1	70293544	70293545	DUP	NA	-	+	[Svaba_SR=22,Svaba_PE=27],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=17]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=JUN|Tier1,CDKN2C|Tier1,JAK1|Tier1,EPS15|Tier1;DisruptL=AC096541.1,TRABD2B;DisruptR=ANKRD13C;Fusion=TRABD2B+ANKRD13C;ClosestL=;ClosestR=	47818752	83866322	18,47818841,70293546	0,0,0
chr1	51383095	51383096	chr1	70292967	70292968	DEL	NA	+	-	[Svaba_SR=30,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=25,Lumpy_SR=1]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=JUN|Tier1,JAK1|Tier1,EPS15|Tier1;DisruptL=EPS15;DisruptR=ANKRD13C;Fusion=ANKRD13C+EPS15;ClosestL=RNU6-877P;ClosestR=	51383049	83866322	0,0,0	0,0,0
chr1	52860644	52860645	chr1	53006333	53006334	DEL	NA	+	-	[Svaba_SR=11,Svaba_PE=21],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=4]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ZYG11A;DisruptR=SCP2;Fusion=ZYG11A+SCP2;ClosestL=;ClosestR=TUBBP10	51383049	51383049	11,52860642,53006332	0,0,0
chr1	54258682	54258683	chr1	54270176	54270177	DEL	NA	+	-	[Svaba_SR=3,Svaba_PE=4],[Lumpy_PE=2,Lumpy_SR=3]	svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SSBP3;DisruptR=SSBP3;ClosestL=SSBP3-AS1;ClosestR=AL161644.1	51383049	51383049	3,54258681,54270175	0,0,0
chr1	58133514	58133515	chr1	58140197	58140198	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=15,Lumpy_SR=12]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=DAB1;DisruptR=DAB1;ClosestL=;ClosestR=	51383049	51383049	15,58133514,58140196	0,0,0
chr1	68760868	68760869	chr6	158632599	158632600	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=8],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=5]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AL033530.1;DisruptR=TMEM181;ClosestL=;ClosestR=DYNLT1	83866322	166890852	0,0,0	0,0,0
chr1	68761024	68761025	chr6	158632373	158632374	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=12],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=17]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AL033530.1;DisruptR=TMEM181;ClosestL=;ClosestR=DYNLT1	83866322	166890852	18,68761023,158632503	0,0,0
chr1	83866390	83866391	chr1	84289947	84289948	DUP	NA	-	+	[Svaba_SR=49,Svaba_PE=57],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=45,Lumpy_SR=33]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=TTLL7;DisruptR=;ClosestL=LINC01725;ClosestR=SAMD13	83866323	84290001	33,83866393,84289949	0,0,0
chr1	94125559	94125560	chr1	94476963	94476964	DUP	NA	-	+	[Svaba_SR=59,Svaba_PE=68],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=54,Lumpy_SR=38]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=ABCD3;ClosestL=ABCA4;ClosestR=	94125488	94476956	39,94125555,94476965	0,0,0
chr1	101718078	101718079	chr20	29887491	29887492	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=34],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=23,Lumpy_SR=9]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC01709;DisruptR=;ClosestL=RNU6-965P;ClosestR=DUX4L37	103478704	29339193	6,101718079,29887491	0,0,0
chr1	101718262	101718263	chr1	107356428	107356429	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=16,Lumpy_SR=9]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC01709;DisruptR=NTNG1;Fusion=LINC01709+NTNG1;ClosestL=RNU6-965P;ClosestR=	103478704	107356812	18,101718263,107356427	0,0,0
chr1	103478736	103478737	chr7	86260442	86260443	TRA	NA	+	+	[Svaba_SR=21,Svaba_PE=20],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=13,Lumpy_SR=13]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC095032.1;DisruptR=;ClosestL=;ClosestR=	103478705	84789193	18,103478737,86260444	0,0,0
chr1	122515320	122515321	chr7	84167768	84167769	TRA	NA	+	-	[Svaba_SR=14,Svaba_PE=7]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=SEMA3A;ClosestL=;ClosestR=	107356813	84167575	0,0,0	0,0,0
chr1	124984581	124984582	chr21	15414727	15414728	TRA	NA	-	-	[Svaba_SR=10,Svaba_PE=4],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AJ009632.2;ClosestL=;ClosestR=	107356813	15873584	0,0,0	0,0,0
chr1	124984643	124984644	chr21	15415109	15415110	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AJ009632.2;ClosestL=;ClosestR=	107356813	15873584	0,0,0	0,0,0
chr1	124984849	124984850	chr21	46035777	46035778	TRA	NA	+	-	[Lumpy_PE=4,Lumpy_SR=1]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=AP001476.1	107356813	46107841	2,124984850,46035775	0,0,0
chr1	143191333	143191334	chr6	32039557	32039558	TRA	NA	+	+	[Svaba_SR=18,Svaba_PE=11]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=CYP21A2;ClosestL=;ClosestR=TNXB	150474751	32487100	14,143191335,32039560	0,0,0
chr1	150474819	150474820	chr1	150749754	150749755	DUP	NA	-	+	[Svaba_SR=42,Svaba_PE=47],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=31,Lumpy_SR=24]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=RPRD2;DisruptR=CTSS;ClosestL=TARS2;ClosestR=	150474752	150749712	30,150474821,150749756	0,0,0
chr1	150980858	150980859	chr1	151012056	151012057	DEL	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=PRUNE1;ClosestL=ANXA9;ClosestR=MINDY1	150749712	150749712	4,150980860,151012056	0,0,0
chr1	155287407	155287408	chr1	155310603	155310604	DEL	NA	+	-	[Svaba_SR=23,Svaba_PE=27],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=16]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HCN3;DisruptR=FDPS;Fusion=HCN3+FDPS;ClosestL=PKLR;ClosestR=RUSC1-AS1	150749712	150749712	16,155287407,155310602	0,0,0
chr1	156727473	156727474	chr1	156728410	156728411	DEL	NA	+	-	[Svaba_SR=3,Svaba_PE=7],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=6,Lumpy_SR=1]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ISG20L2;DisruptR=ISG20L2;ClosestL=RRNAD1;ClosestR=RRNAD1	150749712	150749712	3,156727475,156728409	0,0,0
chr1	186672823	186672824	chr12	67114875	67114876	TRA	NA	-	+	[Svaba_SR=20,Svaba_PE=19],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=9,Lumpy_SR=11]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PTGS2;DisruptR=;ClosestL=PACERR;ClosestR=RAB11AP2	186671317	67920515	15,186672823,67114877	0,0,0
chr1	188617780	188617781	chr3	13545970	13545971	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=FBLN2	186671317	10083194	0,0,0	0,0,0
chr1	188617780	188617781	chr6	144660335	144660336	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=UTRN;ClosestL=;ClosestR=	186671317	130004067	0,0,0	0,0,0
chr1	188617781	188617782	chr21	32343522	32343523	TRA	NA	-	-	[Svaba_SR=22,Svaba_PE=10],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=2,Lumpy_SR=18]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=URB1;ClosestL=;ClosestR=	186671317	32738934	19,188617781,32343521	0,0,0
chr1	188617939	188617940	chr12	67114681	67114682	TRA	NA	+	-	[Svaba_SR=21,Svaba_PE=2],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=2,Lumpy_SR=19]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=RAB11AP2	186671317	67920515	21,188617941,67114680	0,0,0
chr1	198506756	198506757	chr21	14755914	14755915	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=ATP6V1G3;ClosestR=POLR2CP1	203360618	14697623	0,0,0	0,0,0
chr1	200173681	200173682	chr1	200175120	200175121	DEL	NA	+	-	[Svaba_SR=4,Svaba_PE=0]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=NR5A2;DisruptR=NR5A2;ClosestL=;ClosestR=	203360618	203360618	3,200173679,200175119	0,0,0
chr1	200899901	200899902	chr21	7949041	7949042	TRA	NA	-	+	[Svaba_SR=46,Svaba_PE=0]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=INAVA;DisruptR=;ClosestL=MROH3P;ClosestR=	203360618	12966568	40,200899900,7949043	0,0,0
chr1	200900173	200900174	chr10	29373568	29373569	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=2,Lumpy_SR=30]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=INAVA;DisruptR=;ClosestL=MROH3P;ClosestR=	203360618	29240216	17,200900233,29373568	0,0,0
chr1	200900232	200900233	chr5	164930879	164930880	TRA	NA	+	-	[Svaba_SR=76,Svaba_PE=0],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=17,Svaba_PE=22],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=8]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=INAVA;DisruptR=PLCB1;ClosestL=MROH3P;ClosestR=	203360618	8765220	11,200908920,8765270	0,0,0
chr1	200934816	200934817	chr10	29240543	29240544	TRA	NA	+	+	[Svaba_SR=20,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=15]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=MROH3P;DisruptR=;ClosestL=RNU6-704P;ClosestR=	203360618	29240216	19,200934818,29240548	0,0,0
chr1	202013942	202013943	chr1	202424227	202424228	DUP	NA	-	+	[Svaba_SR=19,Svaba_PE=29],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=14]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	18,202013942,202424229	0,0,0
chr1	202223003	202223004	chr1	202475925	202475926	DUP	NA	-	+	[Svaba_SR=21,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=13]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LGR6;DisruptR=PPP1R12B;Fusion=PPP1R12B+LGR6;ClosestL=;ClosestR=AC099336.2	203360618	203360618	16,202223006,202475927	0,0,0
chr1	203360676	203360677	chr1	223431545	223431546	DUP	NA	-	+	[Svaba_SR=90,Svaba_PE=118],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=90,Lumpy_SR=59]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=SLC45A3|Tier1,MDM4|Tier1,ELK4|Tier1;DisruptL=;DisruptR=;ClosestL=AL359837.1;ClosestR=	203360619	223431562	54,203360677,223431550	0,0,0
chr1	203425428	203425429	chr1	203429109	203429110	INV	NA	+	+	[Svaba_SR=26,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=15]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	203360619	203360619	0,0,0	0,0,0
chr1	205097876	205097877	chr1	235138998	235138999	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=29],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=11]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	205097986	234776418	13,205097891,235138997	0,0,0
chr1	209171311	209171312	chr13	108157081	108157082	TRA	NA	+	+	[Svaba_SR=26,Svaba_PE=21],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=13,Lumpy_SR=17]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC092810.2;ClosestR=	212301636	107327740	20,209171312,108157083	0,0,0
chr1	209244791	209244792	chr1	212681433	212681434	DUP	NA	-	+	[Svaba_SR=14,Svaba_PE=28],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=23,Lumpy_SR=7]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=;ClosestL=AC092810.1;ClosestR=BATF3	212301636	212996331	5,209244791,212681444	0,0,0
chr1	211388560	211388561	chr2	104320969	104320970	TRA	NA	-	-	[Svaba_SR=12,Svaba_PE=20],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=12]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC00467;DisruptR=;ClosestL=TRAF5;ClosestR=	212301636	105668984	11,211388547,104320968	0,0,0
chr1	211808734	211808735	chr19	14950825	14950826	TRA	NA	+	+	[Svaba_SR=21,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=10]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LPGAT1;DisruptR=SLC1A6;ClosestL=RF00019;ClosestR=OR7C2	212301636	14687524	17,211808735,14950827	0,0,0
chr1	212301721	212301722	chr6	30029837	30029838	TRA	NA	-	-	[Svaba_SR=62,Svaba_PE=76],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=54,Lumpy_SR=43]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AL360091.3,PPP2R5A;DisruptR=ZNRD1ASP;Fusion=ZNRD1ASP-PPP2R5A;ClosestL=AL360091.2;ClosestR=ETF1P1	212301637	32487100	41,212301724,30029836	0,0,0
chr1	213000165	213000166	chr8	121698470	121698471	TRA	NA	+	-	[Svaba_SR=16,Svaba_PE=22],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=15,Lumpy_SR=8]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ANGEL2;DisruptR=AC104233.1;ClosestL=VASH2;ClosestR=AC104233.2	212996332	121698091	9,213000167,121698467	0,0,0
chr1	217777448	217777449	chr11	29804982	29804983	TRA	NA	-	+	[Svaba_SR=50,Svaba_PE=39],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=29]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SPATA17;DisruptR=AC107973.1;Fusion=AC107973.1-SPATA17;ClosestL=SPATA17-AS1;ClosestR=	217777418	29804998	32,217777448,29804984	0,0,0
chr1	220803994	220803995	chrX	87103995	87103996	TRA	NA	-	-	[Svaba_SR=25,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=18]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=MARC1;DisruptR=;ClosestL=MARC2;ClosestR=	220805515	87103047	21,220803997,87103994	0,0,0
chr1	221676688	221676689	chr7	140930514	140930515	TRA	NA	-	+	[Svaba_SR=28,Svaba_PE=29],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=22]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=AC006006.1	220805516	137445254	21,221676690,140930516	0,0,0
chr1	222787229	222787230	chr1	222795328	222795329	INV	NA	+	+	[Svaba_SR=19,Svaba_PE=23],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=21,Lumpy_SR=11]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=AL392172.1	223431562	223431562	16,222787229,222795330	0,0,0
chr1	222794716	222794717	chr18	73989233	73989234	TRA	NA	-	-	[Svaba_SR=19,Svaba_PE=28],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=24,Lumpy_SR=10]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AC090125.1;ClosestL=;ClosestR=	223431562	73990268	13,222794718,73989232	0,0,0
chr1	234957883	234957884	chr1	235095124	235095125	DUP	NA	-	+	[Svaba_SR=15,Svaba_PE=23],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=8]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AL391832.1,AL391832.2;DisruptR=;ClosestL=;ClosestR=AL732292.1	234776418	234776418	12,234957886,235095126	0,0,0
chr1	234972979	234972980	chr1	235146066	235146067	DUP	NA	-	+	[Svaba_SR=18,Svaba_PE=20],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=16,Lumpy_SR=8]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=RBM34,ARID4B;ClosestL=AL391832.2;ClosestR=TOMM20	234776418	234776418	2,234972981,235146067	0,0,0
chr1	242951989	242951990	chr8	108914122	108914123	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AC104248.1;ClosestL=;ClosestR=	242120887	113801448	0,0,0	0,0,0
chr1	246598539	246598540	chr1	246600082	246600083	DEL	NA	+	-	[Svaba_SR=25,Svaba_PE=29],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=11]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=CNST;DisruptR=CNST;ClosestL=AL591623.1;ClosestR=AL591623.1	248946322	248946322	16,246598539,246600081	0,0,0
chr2	2752746	2752747	chr6	52542329	52542330	TRA	NA	-	-	[Svaba_SR=17,Svaba_PE=22],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=16,Lumpy_SR=11]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=TRAM2;ClosestL=;ClosestR=EFHC1	10005	52679253	15,2752747,52542328	0,0,0
chr2	2752961	2752962	chr14	102959581	102959582	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=CDC42BPB;ClosestL=;ClosestR=	10005	104242963	12,2752963,102959583	0,0,0
chr2	2752962	2752963	chr2	91414359	91414360	DEL	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	2752964	2752965	chr17	35740374	35740375	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=;ClosestR=GAS2L2	10005	36041470	0,0,0	0,0,0
chr2	20726878	20726879	chr2	20774906	20774907	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=8],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=1]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LDAH;DisruptR=LDAH;ClosestL=;ClosestR=	37783334	37783334	5,20726880,20774843	0,0,0
chr2	24579528	24579529	chr2	24695351	24695352	DUP	NA	-	+	[Svaba_SR=27,Svaba_PE=35],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=29,Lumpy_SR=16]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=NCOA1|Tier1;DisruptL=NCOA1;DisruptR=NCOA1;ClosestL=RNA5SP88;ClosestR=RNU6-936P	37783334	37783334	20,24579529,24695353	0,0,0
chr2	33705113	33705114	chr2	33705891	33705892	DEL	NA	+	-	[Lumpy_PE=4,Lumpy_SR=1]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=LINC01317;ClosestR=LINC01317	37783334	37783334	0,0,0	0,0,0
chr2	37825636	37825637	chr17	72487322	72487323	TRA	NA	-	-	[Svaba_SR=20,Svaba_PE=28],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=21,Lumpy_SR=13]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=LINC00511;ClosestL=LINC00211;ClosestR=	37783335	67102560	17,37825628,72487319	0,0,0
chr2	46022801	46022802	chr8	95645038	95645039	TRA	NA	-	-	[Manta_PE=0,Manta_SR=1]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=PRKCE;DisruptR=C8orf37-AS1;ClosestL=AC017078.1;ClosestR=	37783335	96324265	3,46022799,95645038	9,46022800,95645037
chr2	62620842	62620843	chr2	63261205	63261206	DUP	NA	-	+	[Svaba_SR=46,Svaba_PE=46],[Manta_PE=1,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AC092155.1;DisruptR=WDPCP;Fusion=AC092155.1+WDPCP;ClosestL=;ClosestR=	62620651	63608437	0,0,0	0,0,0
chr2	89021117	89021118	chr2	90179484	90179485	INV	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;DisruptL=;DisruptR=;ClosestL=IGKV2-10;ClosestR=IGKV2D-10	94141931	94141931	2,89021129,90179486	0,0,0
chr2	89029964	89029965	chr2	90170598	90170599	INV	NA	+	+	[Manta_PE=0,Manta_SR=23]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;gap;DisruptL=;DisruptR=;ClosestL=IGKV3-11;ClosestR=IGKV3D-11	94141931	94141931	29,89029966,90170600	0,0,0
chr2	91414360	91414361	chr14	102959494	102959495	TRA	NA	-	-	[Svaba_SR=22,Svaba_PE=2],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=CDC42BPB;ClosestL=;ClosestR=	94141931	104242963	4,91414360,102959493	0,0,0
chr2	91414462	91414463	chr17	35740374	35740375	TRA	NA	+	+	[Svaba_SR=25,Svaba_PE=0],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=;ClosestR=GAS2L2	94141931	36041470	17,91414462,35740376	0,0,0
chr2	91414462	91414463	chr3	13545519	13545520	TRA	NA	+	-	[Svaba_SR=47,Svaba_PE=0]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=FBLN2	94141931	10083194	0,0,0	0,0,0
chr2	96997335	96997336	chr11	73060366	73060367	TRA	NA	+	+	[Svaba_SR=25,Svaba_PE=24]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=FCHSD2;ClosestL=AC079395.3;ClosestR=	95642457	74628578	15,96997336,73060368	0,0,0
chr2	99435882	99435883	chr2	103741228	103741229	INV	NA	-	-	[Lumpy_PE=3,Lumpy_SR=1]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=AFF3|Tier1;DisruptL=REV1;DisruptR=;ClosestL=;ClosestR=	95642457	105668984	0,0,0	0,0,0
chr2	99500341	99500342	chr2	101098846	101098847	DEL	NA	+	-	[Svaba_SR=2,Svaba_PE=3],[Lumpy_PE=3,Lumpy_SR=1]	svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=AFF3|Tier1;DisruptL=;DisruptR=TBC1D8;ClosestL=REV1;ClosestR=	95642457	105668984	0,0,0	0,0,0
chr2	99677001	99677002	chr22	24803524	24803525	TRA	NA	-	+	[Svaba_SR=15,Svaba_PE=14],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=10,Lumpy_SR=9]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=AFF3|Tier1;DisruptL=AFF3;DisruptR=;ClosestL=;ClosestR=SGSM1	95642457	23763094	14,99677001,24803526	0,0,0
chr2	99696052	99696053	chr2	99745352	99745353	INV	NA	+	+	[Svaba_SR=10,Svaba_PE=14],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=12,Lumpy_SR=10]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=AFF3|Tier1;DisruptL=AFF3;DisruptR=AFF3;ClosestL=;ClosestR=	95642457	95642457	6,99696052,99745354	0,0,0
chr2	100094212	100094213	chr2	104093617	104093618	INV	NA	-	-	[Svaba_SR=4,Svaba_PE=7],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=1]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=AFF3|Tier1;DisruptL=AFF3;DisruptR=;ClosestL=AC092667.1;ClosestR=LINC01965	95642457	105668984	4,100094213,104093616	0,0,0
chr2	101119639	101119640	chr10	38528506	38528507	TRA	NA	-	-	[Lumpy_PE=11,Lumpy_SR=14]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TBC1D8;DisruptR=;ClosestL=;ClosestR=	105668984	39580116	14,101119642,38528504	0,0,0
chr2	101119899	101119900	chr10	38527881	38527882	TRA	NA	+	-	[Svaba_SR=17,Svaba_PE=28],[Lumpy_PE=19,Lumpy_SR=8]	svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TBC1D8;DisruptR=;ClosestL=;ClosestR=	105668984	39580116	5,101119900,38527880	0,0,0
chr2	103110745	103110746	chr2	103111960	103111961	INV	NA	+	+	[Svaba_SR=19,Svaba_PE=20],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=15]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC073987.1;DisruptR=AC073987.1;ClosestL=;ClosestR=	105668984	105668984	18,103110745,103111962	0,0,0
chr2	103221168	103221169	chr2	103222717	103222718	DUP	NA	-	+	[Lumpy_PE=4,Lumpy_SR=5]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	105668984	105668984	4,103221169,103222718	0,0,0
chr2	103221390	103221391	chr2	103221966	103221967	INV	NA	+	+	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=5]	lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	105668984	105668984	5,103221392,103221968	0,0,0
chr2	104061834	104061835	chr22	49964192	49964193	TRA	NA	-	+	[Svaba_SR=15,Svaba_PE=14],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=7,Lumpy_SR=10]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC01965;DisruptR=;ClosestL=;ClosestR=PIM3	105668984	50808368	13,104061833,49964194	0,0,0
chr2	104063183	104063184	chr22	49963830	49963831	TRA	NA	-	-	[Svaba_SR=18,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=13,Lumpy_SR=11]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC01965;DisruptR=PIM3;ClosestL=;ClosestR=MIR6821	105668984	50808368	14,104063183,49963829	0,0,0
chr2	104240194	104240195	chr16	465006	465007	TRA	NA	+	-	[Svaba_SR=42,Svaba_PE=45],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=26,Lumpy_SR=26]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=RAB11FIP3;ClosestL=;ClosestR=AL049542.1	105668984	10005	27,104240194,465005	0,0,0
chr2	105660629	105660630	chr3	93470608	93470609	TRA	NA	+	-	[Lumpy_PE=3,Lumpy_SR=1]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	105668984	93481450	2,105660629,93470606	0,0,0
chr2	109290685	109290686	chr18	24684289	24684290	TRA	NA	-	+	[Svaba_SR=8,Svaba_PE=16],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=13,Lumpy_SR=5]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SH3RF3;DisruptR=;ClosestL=;ClosestR=RAC1P1	109199785	24684888	5,109290684,24684292	0,0,0
chr2	114725269	114725270	chr18	63805018	63805019	TRA	NA	+	-	[Svaba_SR=11,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=6]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=DPP10;DisruptR=SERPINB7;Fusion=DPP10-SERPINB7;ClosestL=;ClosestR=	114973555	63805005	9,114725273,63805016	0,0,0
chr2	114974129	114974130	chr21	32740681	32740682	TRA	NA	+	+	[Svaba_SR=18,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=11]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=DPP10;DisruptR=PAXBP1-AS1,PAXBP1;Fusion=DPP10-PAXBP1;ClosestL=;ClosestR=SYNJ1	114973556	32738935	2,114974135,32740683	0,0,0
chr2	115753450	115753451	chr22	28669982	28669983	TRA	NA	+	-	[Svaba_SR=12,Svaba_PE=0],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=DPP10;DisruptR=TTC28;ClosestL=;ClosestR=CHEK2	114973556	29406094	9,115753450,28669981	0,0,0
chr2	115753465	115753466	chr22	28670133	28670134	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=8],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=DPP10;DisruptR=TTC28;ClosestL=;ClosestR=CHEK2	114973556	29406094	0,0,0	0,0,0
chr2	135367225	135367226	chr2	135375203	135375204	DEL	NA	+	-	[Svaba_SR=45,Svaba_PE=54],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=28,Lumpy_SR=31]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ZRANB3;DisruptR=ZRANB3;ClosestL=;ClosestR=	114973556	114973556	37,135367224,135375202	0,0,0
chr2	140564947	140564948	chr14	59750331	59750332	TRA	NA	-	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=LRP1B|Tier1;DisruptL=LRP1B;DisruptR=RTN1;Fusion=LRP1B-RTN1;ClosestL=;ClosestR=	114973556	41200381	0,0,0	0,0,0
chr2	142877181	142877182	chr2	142883247	142883248	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=26],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=15,Lumpy_SR=12]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=KYNU;ClosestL=KYNU;ClosestR=	114973556	114973556	10,142877187,142883245	0,0,0
chr2	152347817	152347818	chr2	152457171	152457172	DEL	NA	+	-	[Svaba_SR=28,Svaba_PE=38],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=24]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=FMNL2;DisruptR=FMNL2;ClosestL=;ClosestR=	114973556	114973556	21,152347818,152457170	0,0,0
chr2	165399970	165399971	chr2	166129437	166129438	DUP	NA	-	+	[Svaba_SR=43,Svaba_PE=49],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=35,Lumpy_SR=33]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=AC010127.1,SCN1A;ClosestL=SCN2A;ClosestR=RF00019	114973556	114973556	34,165399973,166129439	0,0,0
chr2	179388075	179388076	chrX	4728101	4728102	TRA	NA	+	-	[Svaba_SR=35,Svaba_PE=40],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC068042.1;ClosestR=	242183395	10446	12,179388069,4728100	0,0,0
chr2	179388334	179388335	chrX	4728528	4728529	TRA	NA	-	+	[Svaba_SR=39,Svaba_PE=40],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=17]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC068042.1;ClosestR=	242183395	10446	22,179388337,4728530	0,0,0
chr2	187258573	187258574	chr11	69848700	69848701	TRA	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC007319.1;DisruptR=;ClosestL=RNU6-989P;ClosestR=	242183395	69779347	19,187258376,69848603	0,0,0
chr2	187552041	187552042	chr2	187556879	187556880	DEL	NA	+	-	[Svaba_SR=16,Svaba_PE=19],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=10,Lumpy_SR=4]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC007319.1,TFPI;DisruptR=TFPI;ClosestL=;ClosestR=AC007319.1	242183395	242183395	19,187552043,187556878	0,0,0
chr2	188399228	188399229	chr5	59193764	59193765	TRA	NA	+	-	[Svaba_SR=10,Svaba_PE=0],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=GULP1;DisruptR=PDE4D;ClosestL=LINC01090;ClosestR=	242183395	32366973	9,188399230,59193763	0,0,0
chr2	194703414	194703415	chr5	69204071	69204072	TRA	NA	+	-	[Svaba_SR=6,Svaba_PE=6]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=CENPH;ClosestL=;ClosestR=MRPS36	242183395	32366973	0,0,0	0,0,0
chr2	218087110	218087111	chr2	218098245	218098246	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=30],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=19]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=RUFY4;DisruptR=;ClosestL=;ClosestR=RUFY4	242183395	242183395	18,218087112,218098244	0,0,0
chr3	9307908	9307909	chr3	9404959	9404960	DUP	NA	-	+	[Svaba_SR=32,Svaba_PE=45],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=42,Lumpy_SR=16]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SRGAP3,AC026191.1;DisruptR=SETD5;ClosestL=;ClosestR=THUMPD3-AS1	9676503	9676503	0,0,0	0,0,0
chr3	9676589	9676590	chr3	10083212	10083213	DUP	NA	-	+	[Svaba_SR=83,Svaba_PE=83],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=56,Lumpy_SR=47]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=FANCD2|Tier1;DisruptL=MTMR14;DisruptR=FANCD2,FANCD2OS;Fusion=FANCD2+MTMR14;ClosestL=;ClosestR=	9676504	10083194	54,9676588,10083214	0,0,0
chr3	13545519	13545520	chr9	72457733	72457734	TRA	NA	-	-	[Svaba_SR=21,Svaba_PE=9],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=15]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=FBLN2;ClosestR=AL445646.1	10083194	65515655	14,13545512,72457732	0,0,0
chr3	13545970	13545971	chr21	32343670	32343671	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=16],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=URB1;ClosestL=FBLN2;ClosestR=	10083194	32738934	0,0,0	0,0,0
chr3	13545970	13545971	chr6	144660231	144660232	TRA	NA	+	-	[Svaba_SR=25,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=7,Lumpy_SR=23]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=UTRN;ClosestL=FBLN2;ClosestR=	10083194	130004067	19,13545972,144660224	0,0,0
chr3	15327029	15327030	chr17	80082215	80082216	TRA	NA	-	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SH3BP5;DisruptR=CCDC40;Fusion=SH3BP5-CCDC40;ClosestL=RNU6-454P;ClosestR=MIR1268B	10083194	83247341	3,15327104,80082244	3,15327104,80082244
chr3	37547039	37547040	chr3	37719792	37719793	DUP	NA	-	+	[Svaba_SR=32,Svaba_PE=38],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=27,Lumpy_SR=21]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ITGA9;DisruptR=ITGA9;ClosestL=;ClosestR=	39770242	39770242	23,37547042,37719794	0,0,0
chr3	39770252	39770253	chr3	41312690	41312691	DUP	NA	-	+	[Svaba_SR=63,Svaba_PE=83],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=69,Lumpy_SR=44]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=CTNNB1|Tier1;DisruptL=;DisruptR=ULK4;ClosestL=;ClosestR=	39770243	41312676	41,39770256,41312692	0,0,0
chr3	41158029	41158030	chr11	80765279	80765280	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=11]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC009743.1;ClosestR=AP002759.1	41312675	80765006	0,0,0	0,0,0
chr3	41158029	41158030	chr14	100903975	100903976	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AL117190.1,MEG8;ClosestL=AC009743.1;ClosestR=RF02146	41312675	104242963	14,41158031,100903977	0,0,0
chr3	41158029	41158030	chrX	87668584	87668585	TRA	NA	+	-	[Svaba_SR=32,Svaba_PE=10],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=KLHL4;ClosestL=AC009743.1;ClosestR=	41312675	87103047	0,0,0	0,0,0
chr3	52565285	52565286	chr3	52629472	52629473	DEL	NA	+	-	[Svaba_SR=45,Svaba_PE=46],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=32,Lumpy_SR=17]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=PBRM1|Tier1;DisruptL=SMIM4,PBRM1;DisruptR=PBRM1;ClosestL=RNU6ATAC16P;ClosestR=	52565238	52629454	23,52565284,52629471	0,0,0
chr3	85183520	85183521	chr3	85187151	85187152	INV	NA	-	-	[Svaba_SR=37,Svaba_PE=29],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=25,Lumpy_SR=29]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=CADM2;DisruptR=CADM2;ClosestL=;ClosestR=	85183522	85183523	34,85183519,85187150	0,0,0
chr3	85660778	85660779	chr3	85663710	85663711	DEL	NA	+	-	[Svaba_SR=42,Svaba_PE=53],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=30,Lumpy_SR=32]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=CADM2;DisruptR=CADM2;ClosestL=;ClosestR=	85183523	85183523	30,85660777,85663709	0,0,0
chr3	91672220	91672221	chr3	95006137	95006138	DUP	NA	-	+	[Svaba_SR=10,Svaba_PE=2]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;DisruptL=;DisruptR=LINC00879;ClosestL=;ClosestR=	93455911	95006071	11,91672224,95006139	0,0,0
chr3	95900220	95900221	chr5	153304740	153304741	TRA	NA	+	-	[Svaba_SR=4,Svaba_PE=7],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=4,Lumpy_SR=2]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	95006071	164930824	4,95900222,153304738	0,0,0
chr3	117319407	117319408	chr3	117323182	117323183	DEL	NA	+	-	[Svaba_SR=23,Svaba_PE=26],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=12]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	95006071	95006071	17,117319408,117323181	0,0,0
chr3	125715063	125715064	chr8	11917891	11917892	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=11]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=OR7E29P;ClosestR=OR7E158P	95006071	71162	3,125715094,11917855	2,125715094,11917855
chr3	126089031	126089032	chr3	126135677	126135678	DEL	NA	+	-	[Svaba_SR=18,Svaba_PE=28],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=21,Lumpy_SR=8]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SLC41A3,AC079848.1;DisruptR=ALDH1L1;Fusion=ALDH1L1+SLC41A3;ClosestL=ALDH1L1;ClosestR=	95006071	95006071	14,126089033,126135676	0,0,0
chr3	132552072	132552073	chr21	16887338	16887339	TRA	NA	+	-	[Svaba_SR=3,Svaba_PE=2]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=ACAD11;ClosestR=AF212831.1	95006071	17474345	2,132552074,16887337	0,0,0
chr3	137757147	137757148	chr5	28238057	28238058	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=SOX14;ClosestR=	170316551	32366972	3,137757192,28237985	3,137757192,28237985
chr3	156596536	156596537	chr20	22251588	22251589	TRA	NA	-	-	[Svaba_SR=18,Svaba_PE=15],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=6]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=LINC01427	170316551	21885645	14,156596535,22251587	0,0,0
chr3	156596713	156596714	chr20	22253039	22253040	TRA	NA	+	-	[Svaba_SR=11,Svaba_PE=16],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=7]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=LINC01427	170316551	21885645	10,156596713,22253038	0,0,0
chr3	170317088	170317089	chr3	195524531	195524532	INV	NA	-	-	[Svaba_SR=23,Svaba_PE=26],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=16,Lumpy_SR=15]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	194247704	19,170317087,195524530	0,0,0
chr3	173507699	173507700	chr3	195524477	195524478	INV	NA	+	+	[Svaba_SR=20,Svaba_PE=26],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=25,Lumpy_SR=4]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	173658862	194247704	14,173507699,195524479	0,0,0
chr3	173507997	173507998	chr3	194247718	194247719	INV	NA	-	-	[Svaba_SR=22,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=2]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=	173658862	194247704	0,0,0	0,0,0
chr3	183359932	183359933	chr5	139904092	139904093	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=16],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=MCF2L2;DisruptR=NRG2;ClosestL=;ClosestR=	173658863	164930824	0,0,0	0,0,0
chr3	184847740	184847741	chr3	184849216	184849217	DEL	NA	+	-	[Svaba_SR=4,Svaba_PE=0],[Lumpy_PE=2,Lumpy_SR=3]	svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=VPS8;DisruptR=VPS8;ClosestL=;ClosestR=	194247703	194247703	3,184847741,184849215	0,0,0
chr3	193906127	193906128	chr3	193912491	193912492	DEL	NA	+	-	[Svaba_SR=49,Svaba_PE=71],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=43,Lumpy_SR=26]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	194247703	194247703	35,193906127,193912490	0,0,0
chr4	7325452	7325453	chr10	51033382	51033383	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=15],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=15]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=84,Svaba_PE=69],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=46,Lumpy_SR=59]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=SORCS2-PRKG1;ClosestL=MIR4798;ClosestR=	10011	39580117	54,7325452,51269342	0,0,0
chr4	7334743	7334744	chr10	50991309	50991310	TRA	NA	-	+	[Svaba_SR=50,Svaba_PE=64],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=45,Lumpy_SR=32]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=PRKG1-SORCS2;ClosestL=;ClosestR=	10011	39580117	32,7334745,50991311	0,0,0
chr4	13541213	13541214	chr4	13542655	13542656	DEL	NA	+	-	[Svaba_SR=25,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=12,Lumpy_SR=18]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=NKX3-2;DisruptR=NKX3-2;ClosestL=LINC01096;ClosestR=LINC01096	14827697	14827697	20,13541212,13542654	0,0,0
chr4	14827425	14827426	chr4	15665086	15665087	DUP	NA	-	+	[Svaba_SR=41,Svaba_PE=38],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=26,Lumpy_SR=24]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC00504;DisruptR=FBXL5;Fusion=LINC00504+FBXL5;ClosestL=;ClosestR=FAM200B	14827697	15665044	32,14827427,15665088	0,0,0
chr4	17613883	17613884	chr12	66979236	66979237	TRA	NA	-	+	[Manta_PE=0,Manta_SR=1]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC006160.1;DisruptR=GRIP1;Fusion=AC006160.1-GRIP1;ClosestL=MED28;ClosestR=	15665044	67920515	0,0,0	0,0,0
chr4	22959992	22959993	chr4	22967233	22967234	DEL	NA	+	-	[Svaba_SR=63,Svaba_PE=76],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=46,Lumpy_SR=39]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;ClosestL=;ClosestR=	15665044	15665044	43,22959992,22967232	0,0,0
chr4	37747941	37747942	chr4	37749092	37749093	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=11]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	52771463	52771463	14,37747943,37749087	0,0,0
chr4	41713489	41713490	chr4	41722276	41722277	DEL	NA	+	-	[Svaba_SR=19,Svaba_PE=21],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=10,Lumpy_SR=10]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=OR5M14P;ClosestR=OR5M14P	52771463	52771463	16,41713489,41722275	0,0,0
chr4	53357081	53357082	chr20	31572616	31572617	TRA	NA	-	-	[Lumpy_PE=2,Lumpy_SR=2]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SCFD2;DisruptR=HM13,HM13-AS1;Fusion=SCFD2-HM13;ClosestL=;ClosestR=AL110115.2	52771464	31539739	2,53357077,31572614	0,0,0
chr4	54132841	54132842	chr4	54134550	54134551	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=13,Lumpy_SR=13]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC058822.1;DisruptR=AC058822.1;ClosestL=;ClosestR=	52771464	52771464	15,54132841,54134549	0,0,0
chr4	57019050	57019051	chr7	56443992	56443993	TRA	NA	-	-	[Svaba_SR=18,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=9,Lumpy_SR=14]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=POLR2B;DisruptR=AC092447.7;Fusion=AC092447.7-POLR2B;ClosestL=IGFBP7;ClosestR=AC092447.10	57019042	57487363	13,57019050,56443991	0,0,0
chr4	59828040	59828041	chr4	59828615	59828616	DEL	NA	+	-	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=45,Lumpy_SR=54]	lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=RF00019;ClosestR=RF00019	59832663	59832663	58,59828042,59828615	0,0,0
chr4	59832640	59832641	chr9	28551943	28551944	TRA	NA	+	-	[Svaba_SR=75,Svaba_PE=85],[Manta_PE=1,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=LINGO2;ClosestL=RF00019;ClosestR=	59832663	28551865	46,59832641,28551942	0,0,0
chr4	65266722	65266723	chr11	69365928	69365929	TRA	NA	+	-	[Svaba_SR=92,Svaba_PE=103],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=58,Lumpy_SR=64]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=MYEOV;ClosestL=;ClosestR=AP005233.2	65266705	69098162	57,65266721,69365927	0,0,0
chr4	74441492	74441493	chr14	98126991	98126992	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AL163932.1;ClosestL=AC021180.1;ClosestR=LINC02295	65266705	104242963	0,0,0	0,0,0
chr4	82823868	82823869	chr8	97238613	97238614	TRA	NA	-	+	[Svaba_SR=35,Svaba_PE=22],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=22]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=SEC31A;DisruptR=;ClosestL=;ClosestR=AP003115.1	91384037	97238482	17,82823867,97238615	0,0,0
chr4	82823983	82823984	chr8	96324292	96324293	TRA	NA	+	-	[Svaba_SR=46,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=10,Lumpy_SR=20]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=SEC31A;DisruptR=PTDSS1;ClosestL=;ClosestR=RF00019	91384037	96324266	24,82823985,96324285	0,0,0
chr4	91384071	91384072	chr18	61626507	61626508	TRA	NA	+	-	[Svaba_SR=47,Svaba_PE=57],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=33,Lumpy_SR=32]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=CCSER1;DisruptR=AC105094.2;ClosestL=;ClosestR=AC090409.1	91384038	61626360	33,91384073,61626505	0,0,0
chr4	91964436	91964437	chr4	91968879	91968880	INV	NA	-	-	[Svaba_SR=39,Svaba_PE=31],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=23]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;ClosestL=;ClosestR=	91964420	91964420	27,91964435,91968878	0,0,0
chr4	92714815	92714816	chr4	92741703	92741704	INV	NA	-	-	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=6,Lumpy_SR=2]	lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=GRID2;DisruptR=GRID2;ClosestL=MTND1P19;ClosestR=	91964420	91964420	3,92714815,92741704	0,0,0
chr4	92714868	92714869	chr4	92741752	92741753	INV	NA	+	+	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=6,Lumpy_SR=2]	manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=GRID2;DisruptR=GRID2;ClosestL=MTND1P19;ClosestR=	91964420	91964420	0,0,0	0,0,0
chr4	182621934	182621935	chr16	80949863	80949864	TRA	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TENM3;DisruptR=;ClosestL=RN7SKP67;ClosestR=CMC2	190066290	90226217	0,0,0	0,0,0
chr4	189021274	189021275	chr4	189022112	189022113	DUP	NA	-	+	[Svaba_SR=17,Svaba_PE=23],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=11]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC122138.1;ClosestR=	190066290	190066290	15,189021273,189022114	0,0,0
chr4	189021849	189021850	chr4	189024736	189024737	DEL	NA	+	-	[Svaba_SR=23,Svaba_PE=32],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=17]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;ClosestL=AC122138.1;ClosestR=	190066290	190066290	19,189021851,189024730	0,0,0
chr5	11509436	11509437	chr10	3336263	3336264	TRA	NA	+	-	[Svaba_SR=14,Svaba_PE=18],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=13,Lumpy_SR=8]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=CTNND2|Tier2;DisruptL=CTNND2;DisruptR=;ClosestL=;ClosestR=	12810903	3335246	6,11509433,3336262	0,0,0
chr5	15633907	15633908	chr5	15634426	15634427	DEL	NA	+	-	[Svaba_SR=5,Svaba_PE=0]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FBXL7;DisruptR=FBXL7;ClosestL=;ClosestR=	12810904	12810904	0,0,0	0,0,0
chr5	23767939	23767940	chr5	23769678	23769679	DEL	NA	+	-	[Svaba_SR=19,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=13]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	32366972	32366972	15,23767941,23769673	0,0,0
chr5	28710819	28710820	chr5	28711436	28711437	DEL	NA	+	-	[Svaba_SR=126,Svaba_PE=92],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=46,Lumpy_SR=49]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	32366972	32366972	0,0,0	0,0,0
chr5	30463531	30463532	chr5	30475422	30475423	DEL	NA	+	-	[Svaba_SR=16,Svaba_PE=27],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=13]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;ClosestL=;ClosestR=	32366972	32366972	12,30463532,30475421	0,0,0
chr5	32366999	32367000	chr10	63904597	63904598	TRA	NA	+	+	[Svaba_SR=42,Svaba_PE=31],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=32]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ZFR;DisruptR=AC022387.1;Fusion=AC022387.1-ZFR;ClosestL=;ClosestR=RPL7AP50	32366973	63904556	31,32367001,63904599	0,0,0
chr5	43171736	43171737	chr5	43188686	43188687	DEL	NA	+	-	[Svaba_SR=11,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=2,Lumpy_SR=4]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ZNF131;DisruptR=ZNF131;ClosestL=;ClosestR=NIM1K	32366973	32366973	10,43171736,43188685	0,0,0
chr5	59193924	59193925	chr10	61749857	61749858	TRA	NA	+	+	[Svaba_SR=3,Svaba_PE=4]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PDE4D;DisruptR=CABCOCO1;Fusion=CABCOCO1-PDE4D;ClosestL=;ClosestR=	32366973	63904555	3,59193926,61749859	0,0,0
chr5	76588049	76588050	chr10	12934286	12934287	TRA	NA	-	+	[Svaba_SR=18,Svaba_PE=11],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=6,Lumpy_SR=15]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=IQGAP2;DisruptR=CCDC3;ClosestL=AC026725.1;ClosestR=RNA5SP300	32366973	3335246	14,76588048,12934288	0,0,0
chr5	76588221	76588222	chr7	43643802	43643803	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=9],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=4,Lumpy_SR=13]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=IQGAP2;DisruptR=COA1;Fusion=IQGAP2-COA1;ClosestL=AC026725.1;ClosestR=STK17A	32366973	43477639	16,76588334,43643804	0,0,0
chr5	78710196	78710197	chr5	78727227	78727228	DEL	NA	+	-	[Svaba_SR=29,Svaba_PE=36],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC008802.1,LHFPL2;DisruptR=LHFPL2;Fusion=LHFPL2+AC008802.1;ClosestL=;ClosestR=AC008802.1	32366973	32366973	21,78710197,78727226	0,0,0
chr5	101330082	101330083	chr5	101342606	101342607	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=23],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=15,Lumpy_SR=15]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	164930824	164930824	18,101330082,101342605	0,0,0
chr5	102801795	102801796	chr5	102874957	102874958	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=20],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PAM;DisruptR=PAM;ClosestL=;ClosestR=	164930824	164930824	0,0,0	0,0,0
chr5	114587648	114587649	chr5	114630660	114630661	DEL	NA	+	-	[Svaba_SR=11,Svaba_PE=14],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=9,Lumpy_SR=8]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC010230.1;DisruptR=AC010230.1;ClosestL=LINC01957;ClosestR=	164930824	164930824	11,114587649,114630649	0,0,0
chr5	114622908	114622909	chr5	114630139	114630140	DEL	NA	+	-	[Svaba_SR=8,Svaba_PE=7],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC010230.1;DisruptR=AC010230.1;ClosestL=;ClosestR=	164930824	164930824	0,0,0	0,0,0
chr5	120820992	120820993	chr5	120828971	120828972	INV	NA	+	+	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=7,Lumpy_SR=6]	lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	164930824	164930824	7,120820994,120828978	0,0,0
chr5	120821054	120821055	chr5	120829449	120829450	INV	NA	-	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	164930824	164930824	2,120821058,120829445	0,0,0
chr5	139904331	139904332	chr7	82672674	82672675	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=21],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=13,Lumpy_SR=18]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=NRG2;DisruptR=;ClosestL=;ClosestR=AC004006.1	164930824	84167574	21,139904402,82672676	0,0,0
chr5	139904402	139904403	chr21	41878046	41878047	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=17],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=NRG2;DisruptR=PRDM15;ClosestL=;ClosestR=AP001619.1	164930824	41822926	0,0,0	0,0,0
chr5	154695628	154695629	chr5	154762331	154762332	DEL	NA	+	-	[Svaba_SR=15,Svaba_PE=22],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=13,Lumpy_SR=8]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=LARP1;ClosestL=MIR1303;ClosestR=	164930824	164930824	12,154695630,154762323	0,0,0
chr5	164930879	164930880	chr10	29373648	29373649	TRA	NA	-	+	[Svaba_SR=45,Svaba_PE=9],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC109466.1;DisruptR=;ClosestL=RNU6-209P;ClosestR=	164930825	29240216	17,164930880,29373650	0,0,0
chr5	166229022	166229023	chr5	176905028	176905029	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=13]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=26,Svaba_PE=5]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=RANBP17;ClosestL=;ClosestR=	164930825	164930825	0,0,0	0,0,0
chr5	166229096	166229097	chr13	103143817	103143818	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=8],[Lumpy_PE=4,Lumpy_SR=7]	svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	164930825	107327739	0,0,0	0,0,0
chr5	169123666	169123667	chr5	171131427	171131428	DUP	NA	-	+	[Svaba_SR=15,Svaba_PE=20],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=9]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SLIT3;DisruptR=RANBP17;ClosestL=;ClosestR=	164930825	164930825	11,169123666,171131429	0,0,0
chr5	170686418	170686419	chr13	104720019	104720020	TRA	NA	-	-	[Svaba_SR=28,Svaba_PE=10],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=KCNIP1;DisruptR=;ClosestL=AC027312.1;ClosestR=	164930825	107327739	0,0,0	0,0,0
chr5	170686434	170686435	chr13	104711356	104711357	TRA	NA	+	+	[Svaba_SR=23,Svaba_PE=12],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=KCNIP1;DisruptR=;ClosestL=AC027312.1;ClosestR=	164930825	107327739	0,0,0	0,0,0
chr5	171130474	171130475	chr5	176905028	176905029	DUP	NA	-	+	[Svaba_SR=22,Svaba_PE=13],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=12,Lumpy_SR=5]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=33,Svaba_PE=5]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=RANBP17;DisruptR=;ClosestL=;ClosestR=	164930825	107327739	0,0,0	0,0,0
chr5	172804771	172804772	chr13	104711181	104711182	TRA	NA	-	-	[Svaba_SR=16,Svaba_PE=12],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=9,Lumpy_SR=8]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC110011.1;ClosestR=	164930825	107327739	12,172804773,104711180	0,0,0
chr5	173535074	173535075	chr21	17229345	17229346	TRA	NA	+	-	[Svaba_SR=15,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=8]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=NEK4P1	180949083	17474345	12,173535079,17229341	0,0,0
chr5	179626987	179626988	chr5	179641488	179641489	INV	NA	+	+	[Svaba_SR=75,Svaba_PE=123],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=109,Lumpy_SR=28]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HNRNPH1;DisruptR=;ClosestL=RF00017;ClosestR=C5orf60	180949083	180949083	49,179626986,179641490	0,0,0
chr6	5651671	5651672	chr7	137445279	137445280	TRA	NA	-	-	[Svaba_SR=24,Svaba_PE=9],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=2,Lumpy_SR=13]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FARS2;DisruptR=DGKI;Fusion=DGKI-FARS2;ClosestL=AL022097.1;ClosestR=	882088	137445254	11,5651672,137445273	0,0,0
chr6	5651753	5651754	chr10	37195827	37195828	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=8],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FARS2;DisruptR=ANKRD30A;Fusion=FARS2-ANKRD30A;ClosestL=AL022097.1;ClosestR=	882088	37167258	6,5651754,37195764	0,0,0
chr6	10615717	10615718	chr6	10671379	10671380	INV	NA	-	-	[Lumpy_PE=5,Lumpy_SR=1]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=GCNT2;DisruptR=;ClosestL=GCNT2P;ClosestR=C6orf52	882088	882088	0,0,0	0,0,0
chr6	24909910	24909911	chr13	23788151	23788152	TRA	NA	+	-	[Svaba_SR=24,Svaba_PE=37],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=27,Lumpy_SR=13]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=RIPOR2;DisruptR=MIPEP;Fusion=MIPEP-RIPOR2;ClosestL=;ClosestR=	24909816	23788156	17,24909912,23788146	0,0,0
chr6	31282776	31282777	chr6	31676535	31676536	DUP	NA	-	+	[Svaba_SR=47,Svaba_PE=52],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=36,Lumpy_SR=6]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=HLA-B;DisruptR=;ClosestL=RPL3P2;ClosestR=LY6G5C	32487100	32487100	32,31282778,31676537	0,0,0
chr6	31341753	31341754	chrX	19326623	19326624	TRA	NA	-	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HLA-B;DisruptR=;ClosestL=MIR6891;ClosestR=PDHA1	32487100	10446	0,0,0	0,0,0
chr6	32646342	32646343	chr22	30015460	30015461	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HLA-DQA1;DisruptR=MTMR3,AC003681.1,HORMAD2-AS1;Fusion=HLA-DQA1-AC003681.1|HLA-DQA1-HORMAD2-AS1;ClosestL=HLA-DQB1;ClosestR=MIR6818	32487101	29406279	6,32646365,30015272	0,0,0
chr6	36092690	36092691	chr11	72659713	72659714	TRA	NA	+	-	[Svaba_SR=24,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=13]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=MAPK14;DisruptR=PDE2A;ClosestL=Z95152.1;ClosestR=AP003065.1	36092705	74628578	18,36092689,72659712	0,0,0
chr6	37947053	37947054	chr6	37948416	37948417	INV	NA	-	-	[Svaba_SR=34,Svaba_PE=49],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=35,Lumpy_SR=19]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ZFAND3;DisruptR=ZFAND3;ClosestL=;ClosestR=	37946969	37946969	0,0,0	0,0,0
chr6	38119595	38119596	chr11	45539585	45539586	TRA	NA	-	-	[Svaba_SR=49,Svaba_PE=57],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=34,Lumpy_SR=37]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ZFAND3;DisruptR=AC103855.2;Fusion=AC103855.2-ZFAND3;ClosestL=;ClosestR=	38141254	45539525	34,38119596,45539584	0,0,0
chr6	38131029	38131030	chr6	38141273	38141274	INV	NA	+	+	[Svaba_SR=42,Svaba_PE=52],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=41,Lumpy_SR=25]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ZFAND3;DisruptR=ZFAND3;ClosestL=;ClosestR=	38141254	38141255	26,38131029,38141275	0,0,0
chr6	38475453	38475454	chr6	38488043	38488044	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=15],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=14]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=BTBD9;DisruptR=BTBD9;ClosestL=BTBD9-AS1;ClosestR=BTBD9-AS1	38141255	38141255	16,38475453,38488042	0,0,0
chr6	48985274	48985275	chr14	47723075	47723076	TRA	NA	-	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	52220478	41200381	0,0,0	0,0,0
chr6	51934058	51934059	chr6	51937863	51937864	INV	NA	+	+	[Svaba_SR=17,Svaba_PE=20],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=12]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PKHD1;DisruptR=PKHD1;ClosestL=;ClosestR=	52220478	52220478	13,51934060,51937865	0,0,0
chr6	52220975	52220976	chr13	110468790	110468791	TRA	NA	-	+	[Svaba_SR=22,Svaba_PE=32],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=14]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=COL4A2;ClosestL=IL17F;ClosestR=COL4A2-AS2	52220479	110418476	17,52220974,110468792	0,0,0
chr6	52542327	52542328	chr14	102959581	102959582	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TRAM2;DisruptR=CDC42BPB;Fusion=TRAM2-CDC42BPB;ClosestL=EFHC1;ClosestR=	52679253	104242963	0,0,0	0,0,0
chr6	52679254	52679255	chr18	23971471	23971472	TRA	NA	+	+	[Svaba_SR=61,Svaba_PE=64],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=43,Lumpy_SR=26]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TMEM14A;DisruptR=AC010754.1;Fusion=TMEM14A-AC010754.1;ClosestL=GSTA8P;ClosestR=LAMA3	52679254	23971375	45,52679253,23971473	0,0,0
chr6	53892612	53892613	chr6	53893328	53893329	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=31],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=22]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LRRC1;DisruptR=LRRC1;ClosestL=;ClosestR=	54303455	54303455	23,53892611,53893327	0,0,0
chr6	54303391	54303392	chr15	76561854	76561855	TRA	NA	+	-	[Svaba_SR=31,Svaba_PE=13],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=6,Lumpy_SR=19]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=SCAPER;ClosestL=TINAG;ClosestR=	54303455	72362590	17,54303392,76561853	0,0,0
chr6	54303391	54303392	chr16	67651996	67651997	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=12]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=CARMIL2;ClosestL=TINAG;ClosestR=ACD	54303455	90226217	0,0,0	0,0,0
chr6	58157667	58157668	chr13	110418585	110418586	TRA	NA	-	+	[Svaba_SR=46,Svaba_PE=65],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=6]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AL445250.1;DisruptR=COL4A2;Fusion=COL4A2-AL445250.1;ClosestL=;ClosestR=AL159153.1	59823890	110418476	34,58157667,110418587	0,0,0
chr6	58190428	58190429	chr11	78640457	78640458	TRA	NA	+	+	[Svaba_SR=52,Svaba_PE=55],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AL445250.1;DisruptR=;ClosestL=;ClosestR=TENM4	59823890	78640469	34,58190430,78640459	0,0,0
chr6	61391894	61391895	chr17	25304748	25304749	TRA	NA	-	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	60241646	22044138	0,0,0	0,0,0
chr6	82898488	82898489	chr6	82899849	82899850	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=19],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=10]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=UBE3D;DisruptR=UBE3D;ClosestL=;ClosestR=	78326602	78326602	16,82898490,82899848	0,0,0
chr6	108428792	108428793	chr6	108701375	108701376	DEL	NA	+	-	[Svaba_SR=15,Svaba_PE=15],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=10,Lumpy_SR=8]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=FOXO3|Tier1;DisruptL=AFG1L;DisruptR=;ClosestL=;ClosestR=FOXO3	129707604	129707604	10,108428791,108701374	0,0,0
chr6	129707662	129707663	chr6	130004047	130004048	DUP	NA	-	+	[Svaba_SR=59,Svaba_PE=89],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=77,Lumpy_SR=36]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ARHGAP18;DisruptR=;ClosestL=;ClosestR=L3MBTL3	129707605	130004066	35,129707665,130004049	0,0,0
chr6	144660335	144660336	chr21	32343657	32343658	TRA	NA	+	+	[Svaba_SR=34,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=4,Lumpy_SR=23]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=UTRN;DisruptR=URB1;Fusion=UTRN-URB1;ClosestL=;ClosestR=	130004067	32738934	21,144660336,32343659	0,0,0
chr6	166891543	166891544	chr16	13287330	13287331	TRA	NA	-	-	[Svaba_SR=13,Svaba_PE=15],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=6]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AL159163.1,RPS6KA2;DisruptR=U91319.1;Fusion=AL159163.1-U91319.1|RPS6KA2-U91319.1;ClosestL=RPS6KA2-AS1;ClosestR=	166890853	13285378	9,166891543,13287329	0,0,0
chr6	168164288	168164289	chr6	168191516	168191517	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=9],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=AL611929.1	166890853	166890853	0,0,0	0,0,0
chr7	1170423	1170424	chr16	5856451	5856452	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=RBFOX1;ClosestL=AC091729.3;ClosestR=AC012175.1	16339	10005	0,0,0	2,1170453,5856274
chr7	29985175	29985176	chr11	76901510	76901511	TRA	NA	-	+	[Svaba_SR=50,Svaba_PE=0]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SCRN1;DisruptR=ACER3;ClosestL=AC007285.1;ClosestR=	43477638	78640469	0,0,0	0,0,0
chr7	29985175	29985176	chr22	28499903	28499904	TRA	NA	-	+	[Svaba_SR=23,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=2,Lumpy_SR=8]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SCRN1;DisruptR=TTC28;Fusion=SCRN1-TTC28;ClosestL=AC007285.1;ClosestR=	43477638	29406094	14,29985176,28499905	0,0,0
chr7	29985277	29985278	chr21	14331478	14331479	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SCRN1;DisruptR=ABCC13;ClosestL=AC007285.1;ClosestR=	43477638	14697622	0,0,0	0,0,0
chr7	43477683	43477684	chr17	67148382	67148383	TRA	NA	-	+	[Svaba_SR=62,Svaba_PE=78],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=48,Lumpy_SR=37]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HECW1;DisruptR=HELZ;ClosestL=;ClosestR=	43477639	67102560	42,43477682,67148384	0,0,0
chr7	44883007	44883008	chr7	44913973	44913974	DUP	NA	-	+	[Svaba_SR=51,Svaba_PE=85],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=67,Lumpy_SR=29]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PURB;DisruptR=;ClosestL=MIR4657;ClosestR=AC004854.1	43477639	43477639	35,44883003,44913976	0,0,0
chr7	47787889	47787890	chr21	13481495	13481496	TRA	NA	-	+	[Svaba_SR=15,Svaba_PE=19],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HUS1,PKD1L1;DisruptR=GTF2IP2;Fusion=HUS1-GTF2IP2|PKD1L1-GTF2IP2;ClosestL=C7orf69;ClosestR=VN1R8P	43477639	12966568	14,47787891,13481497	0,0,0
chr7	47788066	47788067	chr7	57377873	57377874	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=6,Lumpy_SR=8]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=ZNF479|Tier2,EGFR|Tier1,IKZF1|Tier1;DisruptL=HUS1,PKD1L1;DisruptR=;ClosestL=C7orf69;ClosestR=	43477639	57487363	19,47788066,57377872	0,0,0
chr7	53748552	53748553	chr7	53753362	53753363	DEL	NA	+	-	[Svaba_SR=72,Svaba_PE=81],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=43,Lumpy_SR=50]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC01446;DisruptR=LINC01446;ClosestL=;ClosestR=	57487363	57487363	46,53748553,53753361	0,0,0
chr7	57377873	57377874	chr21	13481495	13481496	TRA	NA	-	+	[Svaba_SR=34,Svaba_PE=0]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=GTF2IP2;ClosestL=;ClosestR=VN1R8P	57487363	12966568	0,0,0	0,0,0
chr7	58057425	58057426	chr7	60927101	60927102	DEL	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;ClosestL=;ClosestR=	57497083	62116180	22,58057263,60927264	5,58057263,60927264
chr7	61041202	61041203	chr18	21481531	21481532	TRA	NA	-	-	[Svaba_SR=5,Svaba_PE=3],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=3]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=GREB1L;ClosestL=;ClosestR=	62116180	20553042	3,61041202,21481530	0,0,0
chr7	61053539	61053540	chr7	62344292	62344293	DUP	NA	-	+	[Lumpy_PE=4,Lumpy_SR=1]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;DisruptL=;DisruptR=;ClosestL=;ClosestR=	62116180	62454737	0,0,0	0,0,0
chr7	62742736	62742737	chr8	134414517	134414518	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=2,Lumpy_SR=8]	lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	62742672	145078494	9,62742738,134414519	0,0,0
chr7	62742843	62742844	chr7	87327019	87327020	DEL	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=SBDS|Tier1,ELN|Tier2,HIP1|Tier1,GRM3|Tier2;DisruptL=;DisruptR=TP53TG1;ClosestL=;ClosestR=RF02195	62742672	84789193	0,0,0	0,0,0
chr7	64019531	64019532	chr11	93621875	93621876	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC115220.1;ClosestR=AP003499.1	62742672	80765006	0,0,0	0,0,0
chr7	69920183	69920184	chr7	70236713	70236714	DEL	NA	+	-	[Svaba_SR=7,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=16,Lumpy_SR=10]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AUTS2;DisruptR=AUTS2;ClosestL=;ClosestR=	69920124	70236680	13,69920183,70236712	0,0,0
chr7	82613835	82613836	chr21	41878419	41878420	TRA	NA	-	-	[Svaba_SR=9,Svaba_PE=7],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=8]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=PRDM15;ClosestL=;ClosestR=AP001619.1	84167574	41822926	10,82613834,41878417	0,0,0
chr7	82616051	82616052	chr10	51349321	51349322	TRA	NA	+	-	[Svaba_SR=29,Svaba_PE=7],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=22]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=PRKG1;ClosestL=;ClosestR=	84167574	39580117	21,82616053,51349320	0,0,0
chr7	82672505	82672506	chr21	41878046	41878047	TRA	NA	-	+	[Svaba_SR=35,Svaba_PE=27],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=23]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=PRDM15;ClosestL=AC004006.1;ClosestR=AP001619.1	84167574	41822926	24,82672505,41878048	0,0,0
chr7	86257760	86257761	chr21	26634844	26634845	TRA	NA	-	+	[Svaba_SR=21,Svaba_PE=23],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=14]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	84789193	26634791	15,86257759,26634846	0,0,0
chr7	87327163	87327164	chr8	134414383	134414384	TRA	NA	-	-	[Svaba_SR=20,Svaba_PE=4],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TP53TG1;DisruptR=;ClosestL=RF02195;ClosestR=	84789193	145078494	17,87327163,134414382	0,0,0
chr7	89265302	89265303	chr7	89268691	89268692	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=1]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ZNF804B;DisruptR=ZNF804B;ClosestL=;ClosestR=	84789193	84789193	0,0,0	0,0,0
chr7	92202777	92202778	chr7	92380664	92380665	DEL	NA	+	-	[Svaba_SR=16,Svaba_PE=22],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=16,Lumpy_SR=7]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC000120.1,KRIT1;DisruptR=ANKIB1;ClosestL=RF00019;ClosestR=	84789193	84789193	14,92202778,92380663	0,0,0
chr7	116918744	116918745	chrX	57506628	57506629	TRA	NA	-	+	[Svaba_SR=29,Svaba_PE=34],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=CAPZA2;DisruptR=;ClosestL=RF00019;ClosestR=FAAH2	116918673	57362137	23,116918745,57506630	0,0,0
chr7	137445279	137445280	chr10	37195765	37195766	TRA	NA	-	-	[Svaba_SR=32,Svaba_PE=14],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=18,Svaba_PE=23],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=8]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=BRAF|Tier1;DisruptL=BRAF;DisruptR=;ClosestL=;ClosestR=	137445254	137445254	10,140911266,140955782	0,0,0
chr7	141230709	141230710	chr7	141238330	141238331	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=36],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=15]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TMEM178B;DisruptR=TMEM178B;ClosestL=;ClosestR=	144556895	144556895	19,141230711,141238329	0,0,0
chr7	141234566	141234567	chr7	141311291	141311292	INV	NA	+	+	[Svaba_SR=27,Svaba_PE=27],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=10]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TMEM178B;DisruptR=TMEM178B;ClosestL=;ClosestR=	144556895	144556895	4,141234568,141311293	0,0,0
chr8	10846875	10846876	chr20	47268863	47268864	TRA	NA	-	-	[Svaba_SR=29,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=6,Lumpy_SR=15]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=ZMYND8;ClosestL=AC011008.1;ClosestR=	71162	39349451	19,10846878,47268862	0,0,0
chr8	10847021	10847022	chr20	47225235	47225236	TRA	NA	+	+	[Svaba_SR=22,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=13]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=ZMYND8;ClosestL=AC011008.1;ClosestR=	71162	39349451	17,10847023,47225237	0,0,0
chr8	17875746	17875747	chr11	78407571	78407572	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FGL1;DisruptR=GAB2,AP003086.2;Fusion=AP003086.2-FGL1;ClosestL=AC087273.1;ClosestR=AP003086.3	71162	78640469	5,17875610,78407694	2,17875610,78407694
chr8	38073703	38073704	chr8	38074256	38074257	DEL	NA	+	-	[Svaba_SR=34,Svaba_PE=21],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AP006545.1;ClosestR=AP006545.1	36461421	36461421	18,38073700,38074255	0,0,0
chr8	43475992	43475993	chr11	70550642	70550643	TRA	NA	-	+	[Svaba_SR=200,Svaba_PE=274],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=168,Lumpy_SR=131]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=SHANK2;ClosestL=AC134698.4;ClosestR=	43475933	70550614	88,43475994,70550644	0,0,0
chr8	43634248	43634249	chr8	43635536	43635537	INV	NA	+	+	[Svaba_SR=77,Svaba_PE=42],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=32,Lumpy_SR=24]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	43646293	43646293	37,43634275,43635538	0,0,0
chr8	43646325	43646326	chr14	104763654	104763655	TRA	NA	+	+	[Svaba_SR=107,Svaba_PE=96],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=68,Lumpy_SR=49]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=SIVA1;ClosestL=;ClosestR=AL583722.2	43646294	104242964	62,43646326,104763656	0,0,0
chr8	46943846	46943847	chr8	60480162	60480163	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=27],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=TCEA1|Tier1,PLAG1|Tier1,CHCHD7|Tier1;DisruptL=;DisruptR=LINC01301;ClosestL=AC091163.2;ClosestR=	45740171	60480054	21,46943847,60480161	0,0,0
chr8	47813737	47813738	chr11	58189360	58189361	TRA	NA	-	-	[Svaba_SR=31,Svaba_PE=43],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=31,Lumpy_SR=15]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=PRKDC;DisruptR=OR9Q2;Fusion=PRKDC-OR9Q2;ClosestL=RF00019;ClosestR=OR9Q1	45740171	58828468	22,47813739,58189359	0,0,0
chr8	60642425	60642426	chr8	60724569	60724570	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=30],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=21,Lumpy_SR=8]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=CHD7;ClosestL=AC068389.1;ClosestR=	60480054	60480054	24,60642425,60724568	0,0,0
chr8	80571008	80571009	chr16	22585149	22585150	TRA	NA	-	-	[Svaba_SR=19,Svaba_PE=16]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC009812.2;ClosestR=AC106788.1	69321951	13285378	16,80571008,22585148	0,0,0
chr8	86158943	86158944	chr8	86203823	86203824	INV	NA	+	+	[Svaba_SR=49,Svaba_PE=14],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=4,Lumpy_SR=24]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AC084128.1;ClosestL=ATP6V0D2;ClosestR=SLC7A13	96324265	96324265	19,86158943,86203825	0,0,0
chr8	86159192	86159193	chr8	86204869	86204870	DUP	NA	-	+	[Svaba_SR=21,Svaba_PE=5]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AC084128.1;ClosestL=ATP6V0D2;ClosestR=SLC7A13	96324265	96324265	0,0,0	0,0,0
chr8	86159415	86159416	chr8	86201237	86201238	DEL	NA	+	-	[Svaba_SR=40,Svaba_PE=39],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=29]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=AC084128.1;ClosestL=ATP6V0D2;ClosestR=SLC7A13	96324265	96324265	26,86159417,86201234	0,0,0
chr8	88879692	88879693	chr8	102821044	102821045	INV	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=COX6C|Tier2,NBN|Tier1,CDH17|Tier2,PABPC1|Tier2,RUNX1T1|Tier1,UBR5|Tier1;DisruptL=;DisruptR=;ClosestL=;ClosestR=AZIN1	96324265	101450437	11,88879694,102821046	0,0,0
chr8	88879692	88879693	chr8	88884416	88884417	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=10]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	96324265	96324265	0,0,0	0,0,0
chr8	88884416	88884417	chr8	102820935	102820936	INV	NA	-	-	[Svaba_SR=12,Svaba_PE=7],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=2,Lumpy_SR=3]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=COX6C|Tier2,NBN|Tier1,CDH17|Tier2,PABPC1|Tier2,RUNX1T1|Tier1,UBR5|Tier1;DisruptL=;DisruptR=;ClosestL=;ClosestR=AZIN1	96324265	101450437	8,88884418,102820934	0,0,0
chr8	94880300	94880301	chr8	94902717	94902718	DEL	NA	+	-	[Svaba_SR=30,Svaba_PE=33],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=15,Lumpy_SR=21]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=INTS8,CCNE2;DisruptR=NDUFAF6;Fusion=INTS8+NDUFAF6;ClosestL=AC087752.4;ClosestR=CCNE2	96324265	96324265	24,94880302,94902716	0,0,0
chr8	96324292	96324293	chr8	97238613	97238614	DUP	NA	-	+	[Svaba_SR=72,Svaba_PE=27],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PTDSS1;DisruptR=;ClosestL=RF00019;ClosestR=AP003115.1	96324266	97238482	0,0,0	0,0,0
chr8	101450517	101450518	chr11	69897840	69897841	TRA	NA	-	+	[Svaba_SR=35,Svaba_PE=60],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=38,Lumpy_SR=28]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR=AP007216.1	101450437	69779347	32,101450517,69897842	0,0,0
chr8	101451844	101451845	chr8	113801145	113801146	INV	NA	-	-	[Svaba_SR=0,Svaba_PE=12],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=EIF3E|Tier1,UBR5|Tier1,RSPO2|Tier1,CSMD3|Tier2;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR=	101450437	113801448	3,101451839,113801144	0,0,0
chr8	101451845	101451846	chr11	69897286	69897287	TRA	NA	-	-	[Svaba_SR=60,Svaba_PE=17],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR=AP007216.1	101450437	69779347	0,0,0	0,0,0
chr8	102577651	102577652	chr8	102826803	102826804	DUP	NA	-	+	[Svaba_SR=3,Svaba_PE=6],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=3]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AZIN1;ClosestL=ODF1;ClosestR=GASAL1	101450437	101450437	3,102577656,102826805	0,0,0
chr8	112077674	112077675	chr8	112087837	112087838	DEL	NA	+	-	[Svaba_SR=10,Svaba_PE=19],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=5]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	113801448	113801448	8,112077673,112087836	0,0,0
chr8	113730713	113730714	chr8	113847230	113847231	INV	NA	+	+	[Svaba_SR=43,Svaba_PE=43],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=30,Lumpy_SR=31]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	113801448	113801449	36,113730714,113847232	0,0,0
chr8	113801314	113801315	chr11	69779814	69779815	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=53]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=FGF4	113801448	69779347	0,0,0	0,0,0
chr8	113801314	113801315	chr11	69780162	69780163	TRA	NA	+	+	[Svaba_SR=65,Svaba_PE=79],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=61,Lumpy_SR=35]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=FGF4	113801448	69779347	41,113801316,69780164	0,0,0
chr8	113801461	113801462	chr11	69897286	69897287	TRA	NA	+	-	[Svaba_SR=28,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=21,Lumpy_SR=26]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=AP007216.1	113801449	69779347	24,113801459,69897285	0,0,0
chr8	113817587	113817588	chr8	114411853	114411854	INV	NA	-	-	[Svaba_SR=35,Svaba_PE=32],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=24]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=	113801449	114412377	28,113817589,114411852	0,0,0
chr8	117297894	117297895	chr8	117323013	117323014	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=38],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=21,Lumpy_SR=19]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=;ClosestL=RF00322;ClosestR=RF00322	114412378	114412378	20,117297889,117323012	0,0,0
chr8	118959452	118959453	chr15	76561966	76561967	TRA	NA	-	+	[Svaba_SR=40,Svaba_PE=9]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=SCAPER;ClosestL=TNFRSF11B;ClosestR=	121698090	72362590	0,0,0	0,0,0
chr8	118959452	118959453	chr16	67651851	67651852	TRA	NA	-	-	[Svaba_SR=20,Svaba_PE=0],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=CARMIL2;ClosestL=TNFRSF11B;ClosestR=ACD	121698090	90226217	15,118959451,67651850	0,0,0
chr8	118959598	118959599	chr9	131565190	131565191	TRA	NA	+	+	[Svaba_SR=27,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=17]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=TNFRSF11B;ClosestR=PRRT1B	121698090	138313848	19,118959600,131565192	0,0,0
chr8	122992392	122992393	chr8	123075947	123075948	DEL	NA	+	-	[Svaba_SR=53,Svaba_PE=72],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=47,Lumpy_SR=34]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=TBC1D31;ClosestL=AC104316.2;ClosestR=	121698091	121698091	12,122992391,123075946	0,0,0
chr8	143023980	143023981	chr8	143042570	143042571	DEL	NA	+	-	[Svaba_SR=34,Svaba_PE=50],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=29,Lumpy_SR=25]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=C8orf31;ClosestL=LY6E;ClosestR=AK3P2	145078494	145078494	29,143023978,143042569	0,0,0
chr8	143392048	143392049	chr11	69215633	69215634	TRA	NA	+	-	[Lumpy_PE=3,Lumpy_SR=1]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=RHPN1;ClosestR=	145078494	69098162	6,143392042,69215641	2,143391989,69215631
chr8	144267751	144267752	chr8	144315558	144315559	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=31],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=18]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SCX,BOP1;DisruptR=DGAT1;Fusion=DGAT1+BOP1;ClosestL=MIR7112;ClosestR=AC233992.1	145078494	145078494	17,144267746,144315557	0,0,0
chr9	33983407	33983408	chr20	15018947	15018948	TRA	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=UBAP2;DisruptR=MACROD2;ClosestL=OSTCP8;ClosestR=RNU6-1159P	30540069	8765220	5,33983409,15018946	0,0,0
chr9	72457967	72457968	chr17	1788610	1788611	TRA	NA	+	+	[Svaba_SR=16,Svaba_PE=0],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=SMYD4;ClosestL=AL445646.1;ClosestR=SERPINF1	65515655	168977	11,72457969,1788613	0,0,0
chr9	72457967	72457968	chr17	35740200	35740201	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=12],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=AL445646.1;ClosestR=GAS2L2	65515655	36041470	0,0,0	0,0,0
chr9	113363750	113363751	chr9	113614603	113614604	DUP	NA	-	+	[Svaba_SR=23,Svaba_PE=16],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=3]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=BSPRY;DisruptR=AL162727.3;ClosestL=HDHD3;ClosestR=AL162727.1	138313848	138313848	12,113363742,113614610	0,0,0
chr9	123290032	123290033	chr11	76901313	76901314	TRA	NA	+	-	[Svaba_SR=30,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=9,Lumpy_SR=16]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=ACER3;ClosestL=;ClosestR=	138313848	78640469	22,123290034,76901312	0,0,0
chr9	123290032	123290033	chr22	28499617	28499618	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=18],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=TTC28;ClosestL=;ClosestR=	138313848	29406094	0,0,0	0,0,0
chr9	126949538	126949539	chr9	127070386	127070387	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=18],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=RALGPS1;DisruptR=RALGPS1;ClosestL=;ClosestR=ANGPTL2	138313848	138313848	19,126949537,127070385	0,0,0
chr9	130329753	130329754	chr15	78599746	78599747	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=10]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HMCN2;DisruptR=CHRNA3;ClosestL=;ClosestR=AC067863.2	138313848	72362590	0,0,0	0,0,0
chr9	131564960	131564961	chr13	24968358	24968359	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=20],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=2]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=TPTE2P1;ClosestL=PRRT1B;ClosestR=	138313848	24952568	17,131564960,24968357	0,0,0
chr9	131565190	131565191	chr16	67651850	67651851	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=CARMIL2;ClosestL=PRRT1B;ClosestR=ACD	138313848	90226217	0,0,0	0,0,0
chr10	73043	73044	chr12	68509747	68509748	TRA	NA	+	+	[Svaba_SR=22,Svaba_PE=21],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=7]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TUBB8;DisruptR=;ClosestL=IL9RP2;ClosestR=	10287	67920516	16,73044,68509749	0,0,0
chr10	11555130	11555131	chr22	23938184	23938185	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=USP6NL;DisruptR=;ClosestL=;ClosestR=AP000350.1	3335246	23763094	3,11554925,23938230	0,0,0
chr10	14933901	14933902	chr10	15104286	15104287	DEL	NA	+	-	[Svaba_SR=8,Svaba_PE=6],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=6,Lumpy_SR=2]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=DCLRE1C;DisruptR=RPP38,NMT2;Fusion=NMT2+DCLRE1C;ClosestL=;ClosestR=C10orf111	23965103	23965103	7,14933903,15104284	0,0,0
chr10	23965110	23965111	chr10	27758065	27758066	DUP	NA	-	+	[Svaba_SR=32,Svaba_PE=34],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=23,Lumpy_SR=19]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ABI1|Tier1;DisruptL=KIAA1217;DisruptR=MKX-AS1;Fusion=MKX-AS1+KIAA1217;ClosestL=;ClosestR=MKX	23965104	27756914	26,23965110,27758067	0,0,0
chr10	29469448	29469449	chr10	29471183	29471184	DEL	NA	+	-	[Svaba_SR=9,Svaba_PE=11],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=7]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SVIL-AS1,SVIL;DisruptR=SVIL-AS1,SVIL;ClosestL=;ClosestR=	29240216	29240216	8,29469450,29471176	0,0,0
chr10	31156110	31156111	chr10	31160850	31160851	INV	NA	+	+	[Lumpy_PE=2,Lumpy_SR=4]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	29240216	29240216	3,31156109,31160851	0,0,0
chr10	38921737	38921738	chr10	38922383	38922384	INV	NA	-	-	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=2,Lumpy_SR=2]	lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	39580116	39580116	7,38921740,38922380	0,0,0
chr10	38954387	38954388	chr22	25545395	25545396	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=AL022329.1	39580116	23763094	0,0,0	0,0,0
chr10	50989425	50989426	chr10	51269536	51269537	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=45],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=PRKG1;ClosestL=PRKG1;ClosestR=	39580117	39580117	0,0,0	0,0,0
chr10	50989426	50989427	chr10	51033973	51033974	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=18],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=45,Lumpy_SR=61]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=PRKG1;ClosestL=PRKG1;ClosestR=	39580117	39580117	26,50989429,51034009	0,0,0
chr10	51033384	51033385	chr10	51269618	51269619	DUP	NA	-	+	[Svaba_SR=64,Svaba_PE=20],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=13,Lumpy_SR=22]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PRKG1;DisruptR=PRKG1;ClosestL=;ClosestR=	39580117	39580117	29,51033385,51269620	0,0,0
chr10	51033894	51033895	chr10	51269620	51269621	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=20]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PRKG1;DisruptR=PRKG1;ClosestL=;ClosestR=	39580117	39580117	0,0,0	0,0,0
chr10	52646611	52646612	chr10	52650701	52650702	DUP	NA	-	+	[Lumpy_PE=3,Lumpy_SR=4]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC074327.1;DisruptR=AC074327.1;ClosestL=;ClosestR=	63904555	63904555	3,52646611,52650706	0,0,0
chr10	52646823	52646824	chr10	52650698	52650699	DEL	NA	+	-	[Svaba_SR=27,Svaba_PE=37],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=15,Lumpy_SR=18]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC074327.1;DisruptR=AC074327.1;ClosestL=;ClosestR=	63904555	63904555	17,52646827,52650697	0,0,0
chr10	54306934	54306935	chr10	54494396	54494397	DEL	NA	+	-	[Svaba_SR=23,Svaba_PE=27],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=15,Lumpy_SR=15]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=PCDH15;DisruptR=PCDH15,AL353784.1;ClosestL=;ClosestR=	63904555	63904555	17,54306933,54494395	0,0,0
chr10	87097352	87097353	chr10	87201988	87201989	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=8]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SHLD2;DisruptR=;ClosestL=GLUD1;ClosestR=NUTM2A-AS1	63904556	63904556	21,87097352,87201987	0,0,0
chr10	102637238	102637239	chr10	102638085	102638086	DUP	NA	-	+	[Svaba_SR=17,Svaba_PE=20],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=12,Lumpy_SR=7]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=SUFU;ClosestR=TRIM8	133787316	133787316	10,102637237,102638087	0,0,0
chr10	105020094	105020095	chr10	105041776	105041777	DEL	NA	+	-	[Svaba_SR=16,Svaba_PE=22],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=16,Lumpy_SR=11]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=SORCS3;DisruptR=SORCS3;ClosestL=;ClosestR=	133787316	133787316	13,105020091,105041775	0,0,0
chr10	110813898	110813899	chr11	8158850	8158851	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=RBM20;DisruptR=RIC3;Fusion=RBM20-RIC3;ClosestL=;ClosestR=AC091013.1	133787316	10522050	0,0,0	0,0,0
chr10	118059368	118059369	chr10	118078970	118078971	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=19],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=12,Lumpy_SR=12]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=CASC2;DisruptR=CASC2;ClosestL=RAB11FIP2;ClosestR=	133787316	133787316	13,118059365,118078969	0,0,0
chr10	121577109	121577110	chr16	82374597	82374598	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=FGFR2|Tier1;DisruptL=FGFR2;DisruptR=;ClosestL=;ClosestR=	133787316	90226217	5,121577135,82374426	3,121577135,82374426
chr10	121577186	121577187	chr16	82374166	82374167	TRA	NA	-	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=FGFR2|Tier1;DisruptL=FGFR2;DisruptR=;ClosestL=;ClosestR=	133787316	90226217	2,121577158,82374407	6,121577206,82374342
chr10	124466802	124466803	chr10	124471659	124471660	DEL	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=20,Svaba_PE=26],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=10]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=C10orf90;DisruptR=C10orf90;ClosestL=;ClosestR=	133787316	133787316	15,126525711,126567393	0,0,0
chr10	126526972	126526973	chr10	126555979	126555980	DUP	NA	-	+	[Svaba_SR=20,Svaba_PE=26],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=21,Lumpy_SR=10]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=C10orf90;DisruptR=C10orf90;ClosestL=;ClosestR=	133787316	133787316	13,126526971,126555982	0,0,0
chr11	6030233	6030234	chr11	7289788	7289789	INV	NA	-	-	[Svaba_SR=62,Svaba_PE=52],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=30,Lumpy_SR=38]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=OR56A1;DisruptR=SYT9;Fusion=OR56A1+SYT9;ClosestL=RNA5SP329;ClosestR=	4827728	4827728	43,6030230,7289787	0,0,0
chr11	6378402	6378403	chr11	54541309	54541310	INV	NA	+	+	[Svaba_SR=29,Svaba_PE=36],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=31,Lumpy_SR=16]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=	4827728	54537483	19,6378407,54541313	0,0,0
chr11	8415293	8415294	chr11	8417394	8417395	DEL	NA	+	-	[Svaba_SR=26,Svaba_PE=26],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=15,Lumpy_SR=15]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=STK33;DisruptR=STK33;ClosestL=;ClosestR=	10522050	10522050	17,8415300,8417392	0,0,0
chr11	10522055	10522056	chr11	36593163	36593164	DEL	NA	+	-	[Svaba_SR=39,Svaba_PE=46],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=33,Lumpy_SR=22]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	22,10522054,36593162	0,0,0
chr11	11283180	11283181	chr11	39290286	39290287	DUP	NA	-	+	[Svaba_SR=47,Svaba_PE=57],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=46,Lumpy_SR=22]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=MYOD1|Tier1,FANCF|Tier1,WT1|Tier1,LMO2|Tier1;DisruptL=GALNT18;DisruptR=;ClosestL=;ClosestR=	11283094	39290297	32,11283185,39290288	0,0,0
chr11	12343695	12343696	chr11	49740754	49740755	INV	NA	+	+	[Svaba_SR=36,Svaba_PE=39],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=32,Lumpy_SR=21]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=	12343815	49740713	29,12343696,49740766	0,0,0
chr11	18360996	18360997	chr11	18393125	18393126	DEL	NA	+	-	[Svaba_SR=19,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=11]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=GTF2H1;DisruptR=;ClosestL=;ClosestR=LDHA	12343816	12343816	16,18360997,18393124	0,0,0
chr11	47996838	47996839	chr11	51712926	51712927	INV	NA	-	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;DisruptL=PTPRJ;DisruptR=;ClosestL=PTPRJ-AS1;ClosestR=	48860163	49740713	21,47996839,51712925	0,0,0
chr11	48037649	48037650	chr11	48243138	48243139	INV	NA	+	+	[Svaba_SR=50,Svaba_PE=50],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=51,Lumpy_SR=20]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=PTPRJ;DisruptR=;ClosestL=;ClosestR=OR4X2	48860163	48860163	34,48037651,48243140	0,0,0
chr11	48423266	48423267	chr11	48845188	48845189	INV	NA	-	-	[Svaba_SR=36,Svaba_PE=47],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=29,Lumpy_SR=16]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=;ClosestL=OR4C2P;ClosestR=	48860163	48860163	34,48423265,48845187	0,0,0
chr11	54387407	54387408	chr11	54389567	54389568	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	54537482	54537482	0,0,0	0,0,0
chr11	58190284	58190285	chr11	62369331	62369332	DEL	NA	+	-	[Svaba_SR=35,Svaba_PE=34],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=1]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=FEN1|Tier2,SDHAF2|Tier1;DisruptL=OR9Q2;DisruptR=ASRGL1;Fusion=OR9Q2+ASRGL1;ClosestL=OR9Q1;ClosestR=RCC2P6	58828468	60292696	26,58190284,62369330	0,0,0
chr11	58902609	58902610	chrX	56991096	56991097	TRA	NA	-	-	[Svaba_SR=29,Svaba_PE=19],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=GLYATL2;DisruptR=SPIN3;ClosestL=GLYATL1;ClosestR=AL139397.1	58828469	56991084	0,0,0	0,0,0
chr11	59869579	59869580	chr11	68509921	68509922	DUP	NA	-	+	[Svaba_SR=21,Svaba_PE=9],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=6,Lumpy_SR=5]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	59871621	59871622	chr11	68509680	68509681	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=15,Svaba_PE=22],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=5]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=COL4A2;ClosestL=MS4A2;ClosestR=COL4A2-AS2	60292695	110418476	14,60085405,110454725	0,0,0
chr11	60279269	60279270	chr11	62579531	62579532	INV	NA	+	+	[Svaba_SR=56,Svaba_PE=58],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=41,Lumpy_SR=42]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FEN1|Tier2,SDHAF2|Tier1;DisruptL=;DisruptR=AP002990.1,TUT1;ClosestL=MS4A4A;ClosestR=EEF1G	60292695	60292696	44,60279270,62579533	0,0,0
chr11	60292660	60292661	chr11	60293218	60293219	INV	NA	+	+	[Svaba_SR=14,Svaba_PE=28],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=23,Lumpy_SR=7]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MS4A4A;DisruptR=MS4A4A;ClosestL=;ClosestR=	60292695	60292696	9,60292660,60293220	0,0,0
chr11	63930760	63930761	chr11	63934315	63934316	INV	NA	+	+	[Svaba_SR=40,Svaba_PE=16],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=NAA40;ClosestR=NAA40	65505149	65505149	25,63930729,63934317	0,0,0
chr11	63930765	63930766	chr11	63935810	63935811	INV	NA	-	-	[Svaba_SR=81,Svaba_PE=79],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=48,Lumpy_SR=48]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;ClosestL=NAA40;ClosestR=NAA40	65505149	65505149	47,63930766,63935809	0,0,0
chr11	63930769	63930770	chr11	63931437	63931438	INV	NA	+	+	[Svaba_SR=0,Svaba_PE=37],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=15],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MALAT1;DisruptR=;ClosestL=RF01684;ClosestR=ALG1L8P	65505150	67782059	0,0,0	0,0,0
chr11	65505166	65505167	chr11	68509619	68509620	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=10],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MALAT1;DisruptR=PPP6R3;Fusion=PPP6R3+MALAT1;ClosestL=RF01684;ClosestR=	65505150	69098161	4,65505171,68509512	0,0,0
chr11	65505166	65505167	chr12	33653344	33653345	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=8],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MALAT1;DisruptR=;ClosestL=RF01684;ClosestR=	65505150	56255706	0,0,0	0,0,0
chr11	65511293	65511294	chr12	33652636	33652637	TRA	NA	-	-	[Svaba_SR=24,Svaba_PE=27],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=16]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=SNRPGP19;ClosestR=	65505150	56255706	18,65511296,33652635	0,0,0
chr11	65511687	65511688	chr11	68509833	68509834	DEL	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=32,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=7]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=ALG1L8P;ClosestR=AC005252.1	67782059	125881076	0,0,0	0,0,0
chr11	67780880	67780881	chr12	33653292	33653293	TRA	NA	-	+	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=ALG1L8P;ClosestR=	67782059	56255706	0,0,0	0,0,0
chr11	68509503	68509504	chr12	33653292	33653293	TRA	NA	-	+	[Svaba_SR=36,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=12,Lumpy_SR=27]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PPP6R3;DisruptR=;ClosestL=;ClosestR=	69098161	56255706	30,68509504,33653294	0,0,0
chr11	68509871	68509872	chr12	33653087	33653088	TRA	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PPP6R3;DisruptR=;ClosestL=;ClosestR=	69098161	56255706	0,0,0	0,0,0
chr11	69098215	69098216	chr11	69099668	69099669	INV	NA	-	-	[Svaba_SR=113,Svaba_PE=131],[Manta_PE=1,Manta_SR=1]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TPCN2;DisruptR=TPCN2;ClosestL=AP003071.1;ClosestR=AP003071.1	69098162	69098162	2,69098218,69099667	0,0,0
chr11	69189132	69189133	chr12	108227534	108227535	TRA	NA	-	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=WSCD2;ClosestL=AP003071.2;ClosestR=	69098162	112325530	4,69189098,108227719	0,0,0
chr11	69733949	69733950	chr18	28606934	28606935	TRA	NA	-	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;ClosestL=AP001888.1;ClosestR=	69779346	30130550	2,69733823,28607087	4,69733839,28607095
chr11	69757101	69757102	chr11	69769200	69769201	INV	NA	+	+	[Svaba_SR=0,Svaba_PE=92],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=FGF4;ClosestR=FGF4	69779346	69779346	0,0,0	0,0,0
chr11	69757101	69757102	chr14	21263990	21263991	TRA	NA	+	+	[Svaba_SR=150,Svaba_PE=55],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=92]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=HNRNPC;ClosestL=FGF4;ClosestR=	69779346	21264197	75,69757103,21263992	0,0,0
chr11	69769200	69769201	chr14	21263862	21263863	TRA	NA	+	-	[Svaba_SR=134,Svaba_PE=65],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=90]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=HNRNPC;ClosestL=FGF4;ClosestR=	69779346	21264197	67,69769197,21263861	0,0,0
chr11	73534605	73534606	chr11	73698866	73698867	DUP	NA	-	+	[Svaba_SR=15,Svaba_PE=21],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=4]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FAM168A;DisruptR=RAB6A;Fusion=FAM168A+RAB6A;ClosestL=;ClosestR=	74628578	74628578	6,73534606,73698868	0,0,0
chr11	76901510	76901511	chr22	28499618	28499619	TRA	NA	+	-	[Svaba_SR=39,Svaba_PE=11],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=17]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ACER3;DisruptR=TTC28;ClosestL=;ClosestR=	78640469	29406094	0,0,0	0,0,0
chr11	80765279	80765280	chr14	100903883	100903884	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=12],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AL117190.1,MEG8;ClosestL=AP002759.1;ClosestR=RF02146	80765006	104242963	0,0,0	0,0,0
chr11	80765279	80765280	chrX	87668752	87668753	TRA	NA	+	+	[Svaba_SR=21,Svaba_PE=7],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=4,Lumpy_SR=17]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=KLHL4;ClosestL=AP002759.1;ClosestR=	80765006	87103047	16,80765278,87668754	0,0,0
chr11	121197469	121197470	chr11	121472976	121472977	DUP	NA	-	+	[Svaba_SR=27,Svaba_PE=14],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=9,Lumpy_SR=3]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=SORL1;ClosestL=TECTA;ClosestR=AP000977.1	121197407	121473002	17,121197470,121472978	0,0,0
chr12	25346053	25346054	chr12	25347333	25347334	DUP	NA	-	+	[Svaba_SR=17,Svaba_PE=23],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=13]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	41087	41087	12,25346052,25347335	0,0,0
chr12	29663712	29663713	chrX	49045044	49045045	TRA	NA	+	+	[Manta_PE=1,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=TMTC1;DisruptR=;ClosestL=RPL21P99;ClosestR=TFE3	56255706	47658809	2,29663693,49045024	2,29663686,49045026
chr12	37654140	37654141	chr12	37658683	37658684	DUP	NA	-	+	[Svaba_SR=25,Svaba_PE=20],[Lumpy_PE=25,Lumpy_SR=6]	svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	56255706	56255706	0,0,0	0,0,0
chr12	37654199	37654200	chr12	37658947	37658948	INV	NA	+	+	[Svaba_SR=36,Svaba_PE=11]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	56255706	56255706	0,0,0	0,0,0
chr12	37654200	37654201	chr12	37658674	37658675	DEL	NA	+	-	[Lumpy_PE=6,Lumpy_SR=10]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	56255706	56255706	13,37654199,37658663	0,0,0
chr12	37654605	37654606	chr12	37658765	37658766	INV	NA	-	-	[Svaba_SR=21,Svaba_PE=17],[Lumpy_PE=12,Lumpy_SR=16]	svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	56255706	56255706	18,37654609,37658764	0,0,0
chr12	37654614	37654615	chr12	37658938	37658939	DEL	NA	+	-	[Svaba_SR=19,Svaba_PE=19],[Lumpy_PE=10,Lumpy_SR=6]	lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	56255706	56255706	11,37654612,37658937	0,0,0
chr12	37656929	37656930	chr12	37658031	37658032	DEL	NA	+	-	[Svaba_SR=12,Svaba_PE=4],[Lumpy_PE=5,Lumpy_SR=5]	lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	56255706	56255706	5,37656927,37658030	0,0,0
chr12	37656929	37656930	chr12	38268739	38268740	INV	NA	+	+	[Svaba_SR=18,Svaba_PE=9],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=RF00019	56255706	56255706	0,0,0	0,0,0
chr12	37657372	37657373	chr12	38301158	38301159	INV	NA	-	-	[Svaba_SR=22,Svaba_PE=19],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=12]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=ALG10B	56255706	56255706	18,37657369,38301157	0,0,0
chr12	49263676	49263677	chr12	49265087	49265088	DEL	NA	+	-	[Svaba_SR=15,Svaba_PE=26],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=22,Lumpy_SR=8]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TUBA1C,AC010173.1;DisruptR=TUBA1C;ClosestL=AC125611.3;ClosestR=AC125611.3	56255706	56255706	11,49263672,49265086	0,0,0
chr12	56255681	56255682	chr12	61144864	61144865	DUP	NA	-	+	[Svaba_SR=58,Svaba_PE=84],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=67,Lumpy_SR=37]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=	56255706	61144893	35,56255678,61144869	0,0,0
chr12	65713913	65713914	chr12	112325570	112325571	INV	NA	-	-	[Svaba_SR=106,Svaba_PE=172],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=241,Lumpy_SR=254]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	107,65713916,112325569	0,0,0
chr12	65856872	65856873	chr12	67766189	67766190	DEL	NA	+	-	[Svaba_SR=11,Svaba_PE=26],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=10]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=HMGA2|Tier1;DisruptL=AC090673.1,HMGA2;DisruptR=;ClosestL=;ClosestR=AC022513.1	65713850	67920515	12,65856873,67766188	0,0,0
chr12	66145833	66145834	chr12	66682452	66682453	DUP	NA	-	+	[Svaba_SR=22,Svaba_PE=26],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=14]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC078927.1,TMBIM4;DisruptR=GRIP1;Fusion=AC078927.1+GRIP1|TMBIM4+GRIP1;ClosestL=LLPH-DT;ClosestR=	65713850	65713850	16,66145834,66682454	0,0,0
chr12	66362648	66362649	chr12	68497810	68497811	DUP	NA	-	+	[Svaba_SR=56,Svaba_PE=59],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=46,Lumpy_SR=34]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=GRIP1;DisruptR=;ClosestL=HELB;ClosestR=AC008033.2	65713850	67920516	38,66362649,68497812	0,0,0
chr12	66410668	66410669	chr12	69873475	69873476	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=14],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=12,Lumpy_SR=9]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=MDM2|Tier1;DisruptL=GRIP1;DisruptR=MYRFL;ClosestL=;ClosestR=AC025263.2	65713850	69869147	15,66410665,69873474	0,0,0
chr12	66453482	66453483	chr12	68613971	68613972	DEL	NA	+	-	[Svaba_SR=51,Svaba_PE=48],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=27,Lumpy_SR=36]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=GRIP1;DisruptR=RAP1B;ClosestL=;ClosestR=RPL10P12	65713850	67920516	36,66453484,68613970	0,0,0
chr12	67114680	67114681	chr21	32343521	32343522	TRA	NA	-	-	[Svaba_SR=0,Svaba_PE=12]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=URB1;ClosestL=RAB11AP2;ClosestR=	67920515	32738934	0,0,0	0,0,0
chr12	67919941	67919942	chr12	67923109	67923110	INV	NA	+	+	[Svaba_SR=81,Svaba_PE=88],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=69,Lumpy_SR=59]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;ClosestL=LINC01479;ClosestR=LINC01479	67920515	67920516	26,67919943,67923111	0,0,0
chr12	69782621	69782622	chr12	69869191	69869192	DEL	NA	+	-	[Svaba_SR=177,Svaba_PE=193],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=101,Lumpy_SR=117]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=RAB3IP;DisruptR=MYRFL;Fusion=RAB3IP+MYRFL;ClosestL=AC025263.2;ClosestR=AC025263.2	69782593	69869147	81,69782622,69869190	0,0,0
chr12	69967248	69967249	chr12	70003771	70003772	INV	NA	+	+	[Svaba_SR=19,Svaba_PE=23],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=15]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC025159.1;DisruptR=AC025159.1;ClosestL=MYRFL;ClosestR=	69869147	69869147	16,69967248,70003773	0,0,0
chr12	71972105	71972106	chr12	71993496	71993497	DUP	NA	-	+	[Svaba_SR=19,Svaba_PE=19],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=16,Lumpy_SR=11]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=52,Svaba_PE=58],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=38,Lumpy_SR=34]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=TPH2;DisruptR=TPH2;ClosestL=;ClosestR=	71964314	71964314	35,71975433,72007829	0,0,0
chr12	72510655	72510656	chr12	72511895	72511896	INV	NA	+	+	[Svaba_SR=106,Svaba_PE=137],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=116,Lumpy_SR=74]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=TRHDE;DisruptR=TRHDE;ClosestL=;ClosestR=	72511836	72511837	63,72510657,72511897	0,0,0
chr12	72534503	72534504	chr12	72535081	72535082	DUP	NA	-	+	[Svaba_SR=11,Svaba_PE=6],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=6,Lumpy_SR=6]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TRHDE;DisruptR=TRHDE;ClosestL=;ClosestR=	72511837	72511837	8,72534504,72535083	0,0,0
chr12	96149120	96149121	chr12	96166173	96166174	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=21],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=10,Lumpy_SR=14]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=LINC02452;ClosestL=LINC02452;ClosestR=	112325530	112325530	16,96149120,96166172	0,0,0
chr12	101739295	101739296	chr12	101984856	101984857	DUP	NA	-	+	[Svaba_SR=24,Svaba_PE=20],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=16]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SYCP3,CHPT1;DisruptR=DRAM1;Fusion=DRAM1+CHPT1;ClosestL=GNPTAB;ClosestR=	112325530	112325530	17,101739295,101984858	0,0,0
chr12	112316935	112316936	chr12	112384855	112384856	DUP	NA	-	+	[Svaba_SR=175,Svaba_PE=213],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=170,Lumpy_SR=63]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=HECTD4;DisruptR=;ClosestL=AC004217.2;ClosestR=HECTD4	112325530	112386380	81,112316936,112384857	0,0,0
chr12	112317527	112317528	chr12	112386389	112386390	INV	NA	+	+	[Svaba_SR=101,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=157,Lumpy_SR=117]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HECTD4;DisruptR=;ClosestL=AC004217.2;ClosestR=HECTD4	112325530	112386381	78,112317526,112386391	0,0,0
chr12	112383513	112383514	chr12	112384031	112384032	DEL	NA	+	-	[Svaba_SR=4,Svaba_PE=0]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=HECTD4;ClosestR=HECTD4	112386380	112386380	3,112383532,112384064	0,0,0
chr13	25024466	25024467	chr13	25030471	25030472	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=21],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=12]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;ClosestL=AL590099.1;ClosestR=AL590099.1	24952568	24952568	17,25024465,25030470	0,0,0
chr13	28880457	28880458	chr13	98509424	98509425	DEL	NA	+	-	[Svaba_SR=54,Svaba_PE=61],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=42,Lumpy_SR=27]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	32,28880457,98509423	0,0,0
chr13	97331894	97331895	chr13	97689069	97689070	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=12,Lumpy_SR=16]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=MBNL2;DisruptR=;ClosestL=;ClosestR=AL359502.1	97331911	97689010	16,97331894,97689068	0,0,0
chr13	101085680	101085681	chr13	101107648	101107649	DEL	NA	+	-	[Svaba_SR=20,Svaba_PE=24],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=10]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=NALCN;DisruptR=NALCN;ClosestL=;ClosestR=	98509395	98509395	17,101085680,101107647	0,0,0
chr13	102238357	102238358	chr21	18481781	18481782	TRA	NA	-	+	[Svaba_SR=26,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=16,Lumpy_SR=17]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FGF14;DisruptR=TMPRSS15,AL109763.1;Fusion=FGF14-TMPRSS15|FGF14-AL109763.1;ClosestL=;ClosestR=	98509395	18481760	21,102238356,18481783	0,0,0
chr13	107326514	107326515	chr13	107327081	107327082	INV	NA	-	-	[Svaba_SR=24,Svaba_PE=10]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FAM155A;DisruptR=FAM155A;ClosestL=SNORD31B;ClosestR=SNORD31B	107327739	107327739	4,107326511,107327077	0,0,0
chr13	107326584	107326585	chr18	3047570	3047571	TRA	NA	+	-	[Svaba_SR=23,Svaba_PE=16],[Lumpy_PE=8,Lumpy_SR=9]	svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FAM155A;DisruptR=;ClosestL=SNORD31B;ClosestR=MYOM1	107327739	3047104	4,107326584,3047569	0,0,0
chr13	107327081	107327082	chr18	3047570	3047571	TRA	NA	-	-	[Svaba_SR=33,Svaba_PE=17],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FAM155A;DisruptR=;ClosestL=SNORD31B;ClosestR=MYOM1	107327739	3047104	0,0,0	0,0,0
chr13	107559859	107559860	chr13	108859484	108859485	DUP	NA	-	+	[Lumpy_PE=9,Lumpy_SR=7]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FAM155A;DisruptR=MYO16;ClosestL=;ClosestR=	107327740	107327740	3,107559859,108859485	0,0,0
chr13	107560030	107560031	chr13	108859489	108859490	INV	NA	-	-	[Svaba_SR=19,Svaba_PE=16],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=17]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FAM155A;DisruptR=MYO16;Fusion=FAM155A+MYO16;ClosestL=;ClosestR=	107327740	107327740	17,107560032,108859488	0,0,0
chr13	107560301	107560302	chr13	108954298	108954299	DEL	NA	+	-	[Svaba_SR=30,Svaba_PE=23],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=17]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FAM155A;DisruptR=MYO16;ClosestL=;ClosestR=	107327740	110418475	18,107560301,108954297	0,0,0
chr13	108859137	108859138	chr13	108952144	108952145	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=12],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=9]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR=	107327740	110418475	7,108859329,108952205	0,0,0
chr13	108859285	108859286	chr13	108952396	108952397	DEL	NA	+	-	[Svaba_SR=27,Svaba_PE=0],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR=	107327740	110418475	2,108859287,108952274	0,0,0
chr14	20575192	20575193	chr14	21264283	21264284	DUP	NA	-	+	[Svaba_SR=38,Svaba_PE=44],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=31,Lumpy_SR=26]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=HNRNPC;ClosestL=AL163195.3;ClosestR=	20575159	21264198	28,20575195,21264285	0,0,0
chr14	28611523	28611524	chr22	28670132	28670133	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC02300,TTC28;DisruptR=TTC28;ClosestL=EIF4A1P12;ClosestR=CHEK2	21264198	29406094	0,0,0	0,0,0
chr14	28611560	28611561	chr22	28670089	28670090	TRA	NA	-	-	[Lumpy_PE=4,Lumpy_SR=2]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC02300,TTC28;DisruptR=TTC28;ClosestL=EIF4A1P12;ClosestR=CHEK2	21264198	29406094	0,0,0	0,0,0
chr14	28611570	28611571	chr22	28669722	28669723	TRA	NA	+	-	[Svaba_SR=0,Svaba_PE=21]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC02300,TTC28;DisruptR=TTC28;Fusion=TTC28-LINC02300;ClosestL=EIF4A1P12;ClosestR=CHEK2	21264198	29406094	0,0,0	0,0,0
chr14	32961999	32962000	chr14	32970923	32970924	DEL	NA	+	-	[Svaba_SR=70,Svaba_PE=79],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=45,Lumpy_SR=41]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=NPAS3;DisruptR=NPAS3;ClosestL=;ClosestR=	41140316	41140316	40,32961999,32970922	0,0,0
chr14	41463251	41463252	chr14	41474102	41474103	DEL	NA	+	-	[Svaba_SR=11,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=3]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	41200381	41200381	0,0,0	0,0,0
chr14	81201605	81201606	chr14	81202852	81202853	DUP	NA	-	+	[Svaba_SR=9,Svaba_PE=12],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=5]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=GTF2A1;DisruptR=GTF2A1;ClosestL=SNORA79;ClosestR=SNORA79	91109806	91109806	7,81201605,81202854	0,0,0
chr14	91109951	91109952	chr14	91493414	91493415	DUP	NA	-	+	[Svaba_SR=46,Svaba_PE=53],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=37,Lumpy_SR=34]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=DGLUCY;DisruptR=PPP4R3A;ClosestL=SNORA11B;ClosestR=	91109807	91493434	25,91109952,91493416	0,0,0
chr14	100903884	100903885	chrX	87668584	87668585	TRA	NA	-	-	[Svaba_SR=16,Svaba_PE=3],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=4,Lumpy_SR=10]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AL117190.1,MEG8;DisruptR=KLHL4;ClosestL=RF02146;ClosestR=	104242963	87103047	5,100903895,87668583	0,0,0
chr14	104243055	104243056	chr14	104326293	104326294	INV	NA	-	-	[Svaba_SR=115,Svaba_PE=119],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=81,Lumpy_SR=75]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AL590079.1;DisruptR=;ClosestL=;ClosestR=	104242964	104242964	62,104243056,104326292	0,0,0
chr14	104704163	104704164	chr14	105433354	105433355	DUP	NA	-	+	[Svaba_SR=81,Svaba_PE=92],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=64,Lumpy_SR=55]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=AKT1|Tier1;DisruptL=INF2;DisruptR=TEX22,MTA1;Fusion=TEX22+INF2|MTA1+INF2;ClosestL=AL583722.4;ClosestR=AL928654.1	104242964	104242964	60,104704159,105433356	0,0,0
chr14	105117762	105117763	chr14	105352505	105352506	DUP	NA	-	+	[Svaba_SR=42,Svaba_PE=62],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=42,Lumpy_SR=27]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=PACS2;ClosestL=AL512356.2;ClosestR=AL928654.4	104242964	104242964	31,105117762,105352507	0,0,0
chr14	105352519	105352520	chr14	105353317	105353318	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=9]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PACS2;DisruptR=PACS2;ClosestL=AL928654.4;ClosestR=AL928654.4	104242964	104242964	0,0,0	0,0,0
chr15	21545403	21545404	chr18	67194548	67194549	TRA	NA	+	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC183088.1;ClosestR=	17083473	67194596	14,21545405,67194550	0,0,0
chr15	56746798	56746799	chr15	56751379	56751380	INV	NA	-	-	[Svaba_SR=40,Svaba_PE=59],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=42,Lumpy_SR=24]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AC090517.4;DisruptR=AC090517.4;ClosestL=ZNF280D;ClosestR=ZNF280D	56746779	56746779	29,56746800,56751378	0,0,0
chr15	58982260	58982261	chr16	71832202	71832203	TRA	NA	-	-	[Lumpy_PE=3,Lumpy_SR=1]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=RNF111;DisruptR=;ClosestL=AC025918.2;ClosestR=AC010653.1	56746779	90226217	2,58982263,71832297	2,58982263,71832297
chr15	62473857	62473858	chr15	62474396	62474397	DEL	NA	+	-	[Svaba_SR=4,Svaba_PE=0]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TLN2;DisruptR=TLN2;ClosestL=;ClosestR=	65078451	65078451	4,62473848,62474395	0,0,0
chr15	65803608	65803609	chr18	11294088	11294089	TRA	NA	-	+	[Svaba_SR=28,Svaba_PE=36],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=28,Lumpy_SR=15]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=RAB11A;DisruptR=;ClosestL=DENND4A;ClosestR=	65078452	11293918	20,65803604,11294090	0,0,0
chr15	72000221	72000222	chr15	72362565	72362566	DUP	NA	-	+	[Svaba_SR=43,Svaba_PE=55],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=50,Lumpy_SR=25]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC022872.1,MYO9A;DisruptR=AC009690.1,HEXA;Fusion=MYO9A+AC009690.1|MYO9A+HEXA;ClosestL=;ClosestR=AC009690.2	72000144	72362589	29,72000222,72362567	0,0,0
chr15	76561966	76561967	chr16	67651996	67651997	TRA	NA	+	+	[Svaba_SR=24,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=20]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SCAPER;DisruptR=CARMIL2;Fusion=CARMIL2-SCAPER;ClosestL=;ClosestR=ACD	72362590	90226217	20,76561967,67651998	0,0,0
chr15	84047235	84047236	chr15	84047817	84047818	DEL	NA	+	-	[Manta_PE=1,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC027807.1;ClosestR=AC027807.1	72362590	72362590	30,84047237,84047816	0,0,0
chr15	90417947	90417948	chr22	30281382	30281383	TRA	NA	-	+	[Svaba_SR=3,Svaba_PE=5],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=IQGAP1;DisruptR=;ClosestL=;ClosestR=CASTOR1	101981087	29406279	3,90417949,30281384	0,0,0
chr15	90418089	90418090	chr22	30170524	30170525	TRA	NA	+	-	[Svaba_SR=8,Svaba_PE=4],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=IQGAP1;DisruptR=HORMAD2;Fusion=IQGAP1-HORMAD2;ClosestL=;ClosestR=AC002378.1	101981087	29406279	6,90418088,30170523	0,0,0
chr16	20892	20893	chrX	156019949	156019950	TRA	NA	-	+	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=Z84723.1;DisruptR=AJ271736.1;ClosestL=WASIR2;ClosestR=WASH6P	10005	156030795	11,20893,156019953	0,0,0
chr16	515531	515532	chr17	22058252	22058253	TRA	NA	+	+	[Svaba_SR=13,Svaba_PE=13],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=RAB11FIP3;DisruptR=;ClosestL=LINC00235;ClosestR=ABBA01006766.1	10005	22044138	10,515530,22058254	0,0,0
chr16	3191703	3191704	chr16	3228907	3228908	DEL	NA	+	-	[Svaba_SR=28,Svaba_PE=22],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=6]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=39,Svaba_PE=61],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=37,Lumpy_SR=24]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AC008938.1;DisruptR=;ClosestL=;ClosestR=AC008938.1	34502581	34502581	26,24481254,24513933	0,0,0
chr16	70232878	70232879	chr16	70281139	70281140	DEL	NA	+	-	[Svaba_SR=21,Svaba_PE=18],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SMG1P7;DisruptR=AARS;Fusion=AARS+SMG1P7;ClosestL=EXOSC6;ClosestR=RN7SL279P	90226217	90226217	17,70232878,70281138	0,0,0
chr16	74657090	74657091	chr16	74659686	74659687	DEL	NA	+	-	[Svaba_SR=9,Svaba_PE=15],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=9,Lumpy_SR=8]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=RFWD3|Tier2;DisruptL=RFWD3;DisruptR=RFWD3;ClosestL=TMPOP2;ClosestR=TMPOP2	90226217	90226217	9,74657091,74659685	0,0,0
chr16	76745602	76745603	chr16	76759438	76759439	DEL	NA	+	-	[Svaba_SR=23,Svaba_PE=23],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=19]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	23,76745604,76759437	0,0,0
chr16	89517376	89517377	chr16	89597769	89597770	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=27],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=25,Lumpy_SR=3]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SPG7;DisruptR=;ClosestL=AC092123.1;ClosestR=CPNE7	90226217	90226217	2,89517378,89597852	0,0,0
chr17	1788505	1788506	chr17	35740201	35740202	INV	NA	-	-	[Svaba_SR=18,Svaba_PE=0],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	13,1788505,35740200	0,0,0
chr17	26663486	26663487	chr20	31572795	31572796	TRA	NA	+	+	[Lumpy_PE=2,Lumpy_SR=3]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=HM13,HM13-AS1;ClosestL=;ClosestR=AL110115.2	22044138	31539739	3,26663485,31572796	0,0,0
chr17	26962467	26962468	chr18	15197992	15197993	TRA	NA	+	+	[Lumpy_PE=2,Lumpy_SR=2]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC069061.1;ClosestR=AP005901.3	22044138	11707458	4,26962506,15198106	0,0,0
chr17	34007794	34007795	chr17	34345231	34345232	INV	NA	-	-	[Svaba_SR=49,Svaba_PE=42],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=24,Lumpy_SR=38]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC024610.2,AC004147.4,ASIC2;DisruptR=;ClosestL=AC123769.1;ClosestR=CCL13	34345057	34345058	35,34007794,34345230	0,0,0
chr17	34019945	34019946	chr17	43351893	43351894	DEL	NA	+	-	[Svaba_SR=37,Svaba_PE=50],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=26,Lumpy_SR=26]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	27,34019945,43351892	0,0,0
chr17	35981786	35981787	chr17	35985681	35985682	INV	NA	-	-	[Svaba_SR=13,Svaba_PE=13],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=10,Lumpy_SR=10]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=CCL14,AC244100.2,CCL15-CCL14;ClosestL=CCL16;ClosestR=CCL16	36041470	36041470	10,35981786,35985675	0,0,0
chr17	36183293	36183294	chr17	36184037	36184038	INV	NA	+	+	[Svaba_SR=42,Svaba_PE=52],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=35,Lumpy_SR=28]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC243829.1;DisruptR=AC243829.1;ClosestL=AC243829.2;ClosestR=AC243829.2	36041471	36041471	15,36183291,36184039	0,0,0
chr17	39577411	39577412	chr17	39805140	39805141	DUP	NA	-	+	[Svaba_SR=42,Svaba_PE=47],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=45,Lumpy_SR=3]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=ERBB2|Tier1;DisruptL=;DisruptR=IKZF3;ClosestL=AC009283.1;ClosestR=	39577425	39805110	27,39577413,39805142	0,0,0
chr17	44549222	44549223	chr17	44628027	44628028	DEL	NA	+	-	[Svaba_SR=32,Svaba_PE=33],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=25,Lumpy_SR=15]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=;ClosestL=FZD2;ClosestR=SMCO4P1	43301597	43301597	23,44549223,44628026	0,0,0
chr17	47874904	47874905	chr17	48072313	48072314	DUP	NA	-	+	[Svaba_SR=90,Svaba_PE=106],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=84,Lumpy_SR=33]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=CBX1;ClosestL=AC018521.7;ClosestR=AC004477.3	47874912	48072290	52,47874900,48072315	0,0,0
chr17	55526545	55526546	chr17	55537750	55537751	INV	NA	-	-	[Svaba_SR=0,Svaba_PE=11],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=17]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AC105021.1;ClosestL=AC105021.1;ClosestR=GARSP1	55607901	55607901	20,55526545,55537681	0,0,0
chr17	55526721	55526722	chr21	41571013	41571014	TRA	NA	+	-	[Svaba_SR=19,Svaba_PE=22],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=12,Lumpy_SR=11]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AC105021.1;ClosestR=AP006748.1	55607901	41822925	14,55526722,41571012	0,0,0
chr17	55527606	55527607	chr17	55538276	55538277	INV	NA	+	+	[Svaba_SR=17,Svaba_PE=14],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=13]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC105021.1;DisruptR=AC105021.1;ClosestL=SMIM36;ClosestR=GARSP1	55607901	55607901	14,55527605,55538278	0,0,0
chr17	55537682	55537683	chr21	41571013	41571014	TRA	NA	-	-	[Svaba_SR=26,Svaba_PE=7]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC105021.1;DisruptR=;ClosestL=GARSP1;ClosestR=AP006748.1	55607901	41822925	0,0,0	0,0,0
chr17	55607904	55607905	chr17	59518907	59518908	DUP	NA	-	+	[Svaba_SR=65,Svaba_PE=93],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=70,Lumpy_SR=18]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=RNF43|Tier1,MSI2|Tier1;DisruptL=;DisruptR=LINC01476;ClosestL=;ClosestR=RNU4-13P	55607902	59518847	47,55607906,59518909	0,0,0
chr17	67102576	67102577	chr17	67113691	67113692	INV	NA	-	-	[Svaba_SR=83,Svaba_PE=78],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=48,Lumpy_SR=52]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=HELZ;DisruptR=HELZ;ClosestL=;ClosestR=	67102560	67102560	53,67102576,67113690	0,0,0
chr17	71544176	71544177	chr17	71545941	71545942	DEL	NA	+	-	[Svaba_SR=31,Svaba_PE=27],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=21,Lumpy_SR=9]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	67102560	67102560	0,0,0	0,0,0
chr17	72463523	72463524	chr17	72475017	72475018	DEL	NA	+	-	[Svaba_SR=25,Svaba_PE=26],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=19]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR=	67102560	67102560	22,72463525,72475015	0,0,0
chr17	72463523	72463524	chr17	72534012	72534013	DEL	NA	+	-	[Svaba_SR=35,Svaba_PE=10]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR=	67102560	67102560	0,0,0	0,0,0
chr17	72466028	72466029	chr17	72472943	72472944	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=15,Lumpy_SR=18]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR=	67102560	67102560	24,72466023,72472942	0,0,0
chr17	72474704	72474705	chr17	72485602	72485603	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=29],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=16]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR=	67102560	67102560	17,72474708,72485597	0,0,0
chr17	72475233	72475234	chr17	72534012	72534013	DEL	NA	+	-	[Svaba_SR=22,Svaba_PE=16],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=18]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR=	67102560	67102560	19,72475229,72534011	0,0,0
chr17	72487296	72487297	chrX	116501145	116501146	TRA	NA	+	+	[Svaba_SR=0,Svaba_PE=26],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC00511;DisruptR=;ClosestL=;ClosestR=	67102560	115889294	0,0,0	0,0,0
chr17	72487296	72487297	chrX	76243013	76243014	TRA	NA	+	+	[Svaba_SR=29,Svaba_PE=12],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=18]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=LINC00511;DisruptR=;ClosestL=;ClosestR=RNU6-867P	67102560	76241262	24,72487298,76243019	0,0,0
chr17	81921915	81921916	chr21	14696100	14696101	TRA	NA	-	-	[Svaba_SR=39,Svaba_PE=0],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=28]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MAFG;DisruptR=;ClosestL=SIRT7;ClosestR=	83247341	14697622	30,81921917,14696099	0,0,0
chr17	81922131	81922132	chr21	14696028	14696029	TRA	NA	+	-	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=25,Lumpy_SR=19]	lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MAFG;DisruptR=;ClosestL=AC145207.8;ClosestR=	83247341	14697622	11,81922133,14696027	0,0,0
chr17	81922131	81922132	chr21	14696627	14696628	TRA	NA	+	-	[Svaba_SR=54,Svaba_PE=0],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MAFG;DisruptR=;ClosestL=AC145207.8;ClosestR=	83247341	14697622	0,0,0	0,0,0
chr17	81996893	81996894	chr17	81997849	81997850	DEL	NA	+	-	[Svaba_SR=3,Svaba_PE=2],[Lumpy_PE=2,Lumpy_SR=2]	svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=ASPSCR1|Tier1;DisruptL=ASPSCR1;DisruptR=ASPSCR1;ClosestL=;ClosestR=	83247341	83247341	3,81996896,81997851	0,0,0
chr18	1091199	1091200	chr18	1158740	1158741	DEL	NA	+	-	[Svaba_SR=84,Svaba_PE=100],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=66,Lumpy_SR=26]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AP005328.1;DisruptR=AP005328.1;ClosestL=;ClosestR=AP005265.1	276980	276980	48,1091196,1158739	0,0,0
chr18	1442132	1442133	chr18	1517729	1517730	DEL	NA	+	-	[Svaba_SR=17,Svaba_PE=0]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AC008109.1;ClosestL=;ClosestR=	276980	276980	12,1442132,1517728	0,0,0
chr18	1792586	1792587	chr18	30132066	30132067	DUP	NA	-	+	[Svaba_SR=3,Svaba_PE=5],[Lumpy_PE=4,Lumpy_SR=2]	lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;Cancer_census=SS18|Tier1,ZNF521|Tier1;DisruptL=;DisruptR=;ClosestL=AP005057.1;ClosestR=	3047103	30130551	3,1792587,30132068	0,0,0
chr18	2056157	2056158	chr18	2057225	2057226	INV	NA	+	+	[Svaba_SR=5,Svaba_PE=5],[Lumpy_PE=3,Lumpy_SR=2]	svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AP005230.1;DisruptR=AP005230.1;ClosestL=;ClosestR=	3047103	3047103	4,2056154,2057227	0,0,0
chr18	5693420	5693421	chr18	10125703	10125704	DUP	NA	-	+	[Svaba_SR=16,Svaba_PE=21],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=4]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AP005271.1;ClosestL=;ClosestR=	7909753	11293917	11,5693420,10125705	0,0,0
chr18	8331815	8331816	chr18	8670390	8670391	INV	NA	-	-	[Svaba_SR=15,Svaba_PE=22],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=11]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PTPRM;DisruptR=;ClosestL=;ClosestR=TOMM20P3	7909754	7909754	12,8331814,8670389	0,0,0
chr18	9792146	9792147	chr18	9856621	9856622	DEL	NA	+	-	[Svaba_SR=25,Svaba_PE=29],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=22,Lumpy_SR=13]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=RAB31;DisruptR=RAB31;ClosestL=ZNF415P1;ClosestR=RNA5SP449	11293917	11293917	19,9792147,9856620	0,0,0
chr18	11707492	11707493	chr21	9022992	9022993	TRA	NA	+	-	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=28,Lumpy_SR=1]	manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=GNAL;DisruptR=;ClosestL=;ClosestR=CR392039.2	11707458	12966568	29,11707494,9022991	0,0,0
chr18	14810726	14810727	chr18	14817612	14817613	DEL	NA	+	-	[Svaba_SR=19,Svaba_PE=22],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ANKRD30B;DisruptR=AP006565.1,ANKRD30B;ClosestL=AP006565.1;ClosestR=MIR3156-2	11707458	11707458	15,14810731,14817611	0,0,0
chr18	23307636	23307637	chr20	31539702	31539703	TRA	NA	-	-	[Svaba_SR=129,Svaba_PE=129],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=78,Lumpy_SR=58]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=TMEM241;DisruptR=HM13;Fusion=TMEM241-HM13;ClosestL=;ClosestR=AL110115.1	23307596	31539738	70,23307637,31539701	0,0,0
chr18	24278556	24278557	chr18	24279392	24279393	INV	NA	+	+	[Svaba_SR=29,Svaba_PE=34],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=25,Lumpy_SR=16]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=OSBPL1A;DisruptR=OSBPL1A;ClosestL=;ClosestR=	24279487	24279487	18,24278557,24279394	0,0,0
chr18	49180837	49180838	chr18	49181965	49181966	INV	NA	+	+	[Svaba_SR=15,Svaba_PE=8],[Lumpy_PE=3,Lumpy_SR=8]	lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=DYM;DisruptR=DYM;ClosestL=;ClosestR=	49182019	49182019	8,49180843,49181967	0,0,0
chr18	59214242	59214243	chr18	59217204	59217205	DUP	NA	-	+	[Svaba_SR=15,Svaba_PE=16],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=10,Lumpy_SR=11]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=GRP;ClosestR=GRP	59280727	59280727	14,59214241,59217206	0,0,0
chr18	59281023	59281024	chr18	60359158	60359159	DEL	NA	+	-	[Svaba_SR=12,Svaba_PE=2],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=13]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=CPLX4;DisruptR=;ClosestL=RAX;ClosestR=MC4R	59280728	59280728	12,59281019,60359157	0,0,0
chr19	8257771	8257772	chr22	24989957	24989958	TRA	NA	-	-	[Svaba_SR=7,Svaba_PE=0],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=CERS4;DisruptR=KIAA1671;ClosestL=AC022146.2;ClosestR=AL022323.3	12858960	23763094	6,8257772,24989956	0,0,0
chr19	8258007	8258008	chr22	24987321	24987322	TRA	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=CERS4;DisruptR=KIAA1671;Fusion=CERS4-KIAA1671;ClosestL=AC022146.2;ClosestR=	12858960	23763094	7,8258009,24987320	0,0,0
chr19	12858913	12858914	chr19	12880038	12880039	DEL	NA	+	-	[Svaba_SR=75,Svaba_PE=77],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=41,Lumpy_SR=50]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HOOK2,MAST1;DisruptR=DNASE2;Fusion=DNASE2+HOOK2;ClosestL=MIR6794;ClosestR=AC020934.2	12858960	12880013	31,12858913,12880037	0,0,0
chr19	14687538	14687539	chr19	14928275	14928276	INV	NA	-	-	[Svaba_SR=65,Svaba_PE=26],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ADGRE3;DisruptR=;ClosestL=ZNF333;ClosestR=OR7A15P	14687524	14687524	9,14687533,14928268	0,0,0
chr19	14707775	14707776	chr19	14913582	14913583	DUP	NA	-	+	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=97,Lumpy_SR=7]	lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=37,Svaba_PE=42],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=31,Lumpy_SR=15]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=BRD4|Tier1;DisruptL=;DisruptR=AC005785.1;ClosestL=OR7A15P;ClosestR=AKAP8L	14687524	15684658	22,14928302,15379942	0,0,0
chr19	15195290	15195291	chr19	15634353	15634354	DUP	NA	-	+	[Svaba_SR=0,Svaba_PE=13],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=9,Lumpy_SR=9]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=BRD4|Tier1;DisruptL=NOTCH3;DisruptR=;ClosestL=MIR6795;ClosestR=CYP4F8	15684658	15684658	10,15195292,15634435	0,0,0
chr19	15329197	15329198	chr19	20490430	20490431	INV	NA	+	+	[Svaba_SR=37,Svaba_PE=43],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=31,Lumpy_SR=14]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	20502055	27,15329201,20490432	0,0,0
chr19	15384118	15384119	chr19	15506506	15506507	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=31],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=22,Lumpy_SR=11]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AKAP8L;DisruptR=;ClosestL=AC005785.2;ClosestR=CYP4F22	15684658	15684658	18,15384120,15506505	0,0,0
chr19	15523081	15523082	chr19	15546350	15546351	INV	NA	-	-	[Svaba_SR=61,Svaba_PE=55],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=CYP4F22;DisruptR=CYP4F22;ClosestL=AC011492.1;ClosestR=CYP4F23P	15684658	15684658	41,15523081,15546349	0,0,0
chr19	15533868	15533869	chr19	15684645	15684646	INV	NA	+	+	[Svaba_SR=187,Svaba_PE=96],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=149,Lumpy_SR=139]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=CYP4F22;DisruptR=CYP4F12;ClosestL=AC011492.1;ClosestR=CYP4F10P	15684658	15684658	92,15533870,15684647	0,0,0
chr19	15588870	15588871	chr19	15589780	15589781	DEL	NA	+	-	[Svaba_SR=109,Svaba_PE=149],[Manta_PE=1,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=CYP4F23P;ClosestR=CYP4F23P	15684658	15684658	79,15588872,15589779	0,0,0
chr19	15632140	15632141	chr19	20137691	20137692	DEL	NA	+	-	[Svaba_SR=53,Svaba_PE=34],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=36,Lumpy_SR=1]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=TPM4|Tier1,JAK3|Tier1,ELL|Tier1,CRTC1|Tier1;DisruptL=;DisruptR=AC011447.2,AC011447.3;ClosestL=CYP4F8;ClosestR=BNIP3P15	15684658	20137238	38,15632139,20137686	0,0,0
chr19	17316666	17316667	chr19	17362636	17362637	DEL	NA	+	-	[Svaba_SR=5,Svaba_PE=8],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=7,Lumpy_SR=2]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=DDA1;DisruptR=AC010463.2,PLVAP;Fusion=DDA1+AC010463.2;ClosestL=ABHD8;ClosestR=GTPBP3	15684659	15684659	3,17316668,17362634	0,0,0
chr19	20300586	20300587	chr19	20303756	20303757	DEL	NA	+	-	[Svaba_SR=23,Svaba_PE=25],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=9]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC078899.4,AC011447.3;DisruptR=AC078899.4,AC011447.3;ClosestL=;ClosestR=	20137238	20137238	6,20300585,20303755	0,0,0
chr19	20441327	20441328	chr19	20443259	20443260	DEL	NA	+	-	[Svaba_SR=85,Svaba_PE=78],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=45,Lumpy_SR=12]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC008554.1;DisruptR=BNIP3P23,AC008554.1;ClosestL=BNIP3P23;ClosestR=ZNF826P	20502055	20502055	47,20441329,20443254	0,0,0
chr19	20497266	20497267	chr19	20498447	20498448	INV	NA	+	+	[Svaba_SR=36,Svaba_PE=50],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=46,Lumpy_SR=22]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR=	20502055	20502055	25,20497268,20498449	0,0,0
chr19	20497437	20497438	chr19	20501960	20501961	DUP	NA	-	+	[Svaba_SR=35,Svaba_PE=44],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=34,Lumpy_SR=9]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR=	20502055	20502055	26,20497438,20501962	0,0,0
chr19	20498993	20498994	chr19	20507532	20507533	DUP	NA	-	+	[Svaba_SR=32,Svaba_PE=36],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=31,Lumpy_SR=15]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR=	20502055	20502056	20,20498993,20507534	0,0,0
chr19	20506933	20506934	chr19	24352249	24352250	DUP	NA	-	+	[Svaba_SR=37,Svaba_PE=38],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=27,Lumpy_SR=7]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=ZNF429|Tier2;DisruptL=AC008554.1;DisruptR=;ClosestL=;ClosestR=	20502056	24014085	17,20506933,24352272	0,0,0
chr19	23544107	23544108	chr19	23692933	23692934	INV	NA	-	-	[Svaba_SR=17,Svaba_PE=14],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ZNF675;DisruptR=;ClosestL=;ClosestR=ZNF675	23543310	23543310	0,0,0	0,0,0
chr19	24348141	24348142	chr19	24353031	24353032	INV	NA	-	-	[Svaba_SR=35,Svaba_PE=31],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=21,Lumpy_SR=21]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	24014085	24014085	27,24348141,24353030	0,0,0
chr19	24373673	24373674	chr19	24375338	24375339	DEL	NA	+	-	[Svaba_SR=34,Svaba_PE=48],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	24014085	24014085	23,24373656,24375337	0,0,0
chr20	14979685	14979686	chr20	15078263	15078264	DEL	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MACROD2;DisruptR=MACROD2;ClosestL=;ClosestR=	8765220	8765220	6,14979687,15078263	0,0,0
chr20	14979687	14979688	chr20	15067579	15067580	DEL	NA	+	-	[Svaba_SR=0,Svaba_PE=8]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MACROD2;DisruptR=MACROD2;ClosestL=;ClosestR=	8765220	8765220	0,0,0	0,0,0
chr20	15067580	15067581	chr20	15078347	15078348	DUP	NA	-	+	[Svaba_SR=2,Svaba_PE=5]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MACROD2;DisruptR=MACROD2;ClosestL=;ClosestR=	8765220	8765220	2,15067585,15078349	0,0,0
chr20	18763090	18763091	chr20	18763944	18763945	INV	NA	-	-	[Svaba_SR=4,Svaba_PE=3],[Lumpy_PE=2,Lumpy_SR=2]	svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=DTD1;DisruptR=DTD1;ClosestL=AL121900.2;ClosestR=EEF1A1P34	21885644	21885644	4,18763090,18763943	0,0,0
chr20	26330213	26330214	chr20	26331691	26331692	DEL	NA	+	-	[Svaba_SR=12,Svaba_PE=24],[Manta_PE=0,Manta_SR=1]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	28506070	28506070	11,26330156,26331690	0,0,0
chr20	36914523	36914524	chr20	36933537	36933538	INV	NA	+	+	[Svaba_SR=22,Svaba_PE=29],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=17]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=SAMHD1;DisruptR=SAMHD1;ClosestL=;ClosestR=	37368800	37368800	14,36914523,36933539	0,0,0
chr20	47103302	47103303	chr20	47104389	47104390	DEL	NA	+	-	[Svaba_SR=24,Svaba_PE=17],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=EYA2;DisruptR=EYA2;ClosestL=;ClosestR=	39349451	39349451	0,0,0	0,0,0
chr20	47104389	47104390	chr20	47225243	47225244	DUP	NA	-	+	[Lumpy_PE=2,Lumpy_SR=5]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=EYA2;DisruptR=ZMYND8;ClosestL=;ClosestR=	39349451	39349451	3,47104393,47225244	0,0,0
chr20	47225235	47225236	chr20	47268863	47268864	DEL	NA	+	-	[Svaba_SR=45,Svaba_PE=14],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ZMYND8;DisruptR=ZMYND8;ClosestL=;ClosestR=	39349451	39349451	0,0,0	0,0,0
chr20	48179660	48179661	chr20	48180192	48180193	DEL	NA	+	-	[Lumpy_PE=12,Lumpy_SR=15]	lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	39349451	39349451	18,48179660,48180191	0,0,0
chr21	9888809	9888810	chr21	21141002	21141003	DEL	NA	+	-	[Svaba_SR=11,Svaba_PE=14],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;DisruptL=;DisruptR=NCAM2;ClosestL=RN7SL52P;ClosestR=	12966568	20113684	10,9888810,21141001	0,0,0
chr21	10328063	10328064	chr21	10333401	10333402	DUP	NA	-	+	[Svaba_SR=20,Svaba_PE=9]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=AP003900.1;ClosestL=AP003900.1;ClosestR=EIF3FP1	12966568	12966568	15,10328062,10333403	0,0,0
chr21	10561920	10561921	chr21	20715590	20715591	INV	NA	+	+	[Svaba_SR=6,Svaba_PE=3]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;DisruptL=TPTE,AF254983.1;DisruptR=;ClosestL=CYCSP41;ClosestR=	12966568	20113684	0,0,0	0,0,0
chr21	10570015	10570016	chr21	20715590	20715591	INV	NA	+	+	[Svaba_SR=9,Svaba_PE=2],[Manta_PE=0,Manta_SR=0]	manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;DisruptL=TPTE,AF254983.1;DisruptR=;ClosestL=CYCSP41;ClosestR=	12966568	20113684	0,0,0	0,0,0
chr21	13283045	13283046	chr21	13506275	13506276	DEL	NA	+	-	[Svaba_SR=65,Svaba_PE=67],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=GTF2IP2	12966568	12966568	45,13283046,13506274	0,0,0
chr21	14696103	14696104	chr21	14696626	14696627	DEL	NA	+	-	[Manta_PE=0,Manta_SR=0]	manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=;ClosestR=	14697622	14697622	11,14696105,14696625	0,0,0
chr21	15873590	15873591	chr21	16679496	16679497	INV	NA	+	+	[Svaba_SR=124,Svaba_PE=111],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=105,Lumpy_SR=76]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=USP25;DisruptR=;ClosestL=;ClosestR=	15873585	17474345	3,15873593,16679497	0,0,0
chr21	16672953	16672954	chr21	17986177	17986178	DUP	NA	-	+	[Svaba_SR=112,Svaba_PE=119],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=81,Lumpy_SR=79]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=CHODL;ClosestL=;ClosestR=	15873585	17986205	66,16672958,17986179	0,0,0
chr21	17474427	17474428	chr21	41078325	41078326	DUP	NA	-	+	[Svaba_SR=124,Svaba_PE=155],[Manta_PE=1,Manta_SR=1]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=OLIG2|Tier1,RUNX1|Tier1,ERG|Tier1;DisruptL=;DisruptR=;ClosestL=;ClosestR=	17474346	41078299	68,17474426,41078327	0,0,0
chr21	17592650	17592651	chr21	17621842	17621843	DUP	NA	-	+	[Svaba_SR=27,Svaba_PE=27],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=15]	manta,svaba,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=CXADR;DisruptR=BTG3-AS1;Fusion=BTG3-AS1+CXADR;ClosestL=BTG3;ClosestR=BTG3	17474346	17474346	21,17592651,17621844	0,0,0
chr21	18583949	18583950	chr21	18584487	18584488	INV	NA	-	-	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=6]	lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MIR548XHG;DisruptR=MIR548XHG;ClosestL=;ClosestR=	18481760	18481760	3,18583949,18584479	0,0,0
chr21	31947365	31947366	chr21	45927270	45927271	INV	NA	-	-	[Svaba_SR=0,Svaba_PE=44],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	0,0,0	0,0,0
chr21	34819613	34819614	chr21	34850895	34850896	DEL	NA	+	-	[Svaba_SR=28,Svaba_PE=35],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=22]	svaba,manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=RUNX1|Tier1;DisruptL=RUNX1;DisruptR=RUNX1;ClosestL=;ClosestR=	34819639	34847755	22,34819611,34850894	0,0,0
chr21	40764315	40764316	chr21	44064619	44064620	INV	NA	-	-	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=100,Lumpy_SR=51]	manta,lumpy	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;Cancer_census=TMPRSS2|Tier1,U2AF1|Tier1;DisruptL=DSCAM;DisruptR=TRAPPC10;Fusion=DSCAM+TRAPPC10;ClosestL=;ClosestR=H2AFZP1	40764260	44064550	2,40764313,44064621	0,0,0
chr21	41822940	41822941	chr21	42103805	42103806	DUP	NA	-	+	[Svaba_SR=91,Svaba_PE=99],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=92,Lumpy_SR=55]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PRDM15;DisruptR=UMODL1-AS1,UMODL1;Fusion=PRDM15+UMODL1-AS1;ClosestL=;ClosestR=	41822926	42103808	55,41822941,42103807	0,0,0
chr21	41823975	41823976	chr21	46107855	46107856	INV	NA	+	+	[Svaba_SR=108,Svaba_PE=120],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=104,Lumpy_SR=47]	lumpy,manta,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;Cancer_census=U2AF1|Tier1;DisruptL=PRDM15;DisruptR=COL6A2;Fusion=COL6A2+PRDM15;ClosestL=;ClosestR=AP001471.1	41822926	46107842	63,41823975,46107857	0,0,0
chr21	41825929	41825930	chr21	45927312	45927313	DUP	NA	-	+	[Svaba_SR=72,Svaba_PE=148],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=133,Lumpy_SR=25]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;gap;Cancer_census=U2AF1|Tier1;DisruptL=PRDM15;DisruptR=PCBP3;ClosestL=;ClosestR=AJ239328.1	41822926	46107841	29,41825930,45927314	0,0,0
chr21	41831216	41831217	chr21	41833962	41833963	DEL	NA	+	-	[Svaba_SR=109,Svaba_PE=123],[Manta_PE=1,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=PRDM15;DisruptR=PRDM15;ClosestL=;ClosestR=	41822926	41822926	61,41831218,41833961	0,0,0
chr21	42948646	42948647	chr21	42950135	42950136	DEL	NA	+	-	[Svaba_SR=51,Svaba_PE=51],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=34,Lumpy_SR=22]	svaba,lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=MIR5692B;ClosestR=MIR5692B	42103809	42103809	35,42948644,42950134	0,0,0
chr22	16812440	16812441	chr22	27132898	27132899	INV	NA	-	-	[Manta_PE=0,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=4]	lumpy,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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	29406094	5,16812445,27132893	0,0,0
chr22	17097645	17097646	chr22	17098740	17098741	INV	NA	+	+	[Svaba_SR=10,Svaba_PE=12],[Manta_PE=0,Manta_SR=0]	svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=IL17RA;DisruptR=IL17RA;ClosestL=AC006946.1;ClosestR=AC006946.1	10514978	10514978	0,0,0	0,0,0
chr22	20476966	20476967	chr22	20591962	20591963	DEL	NA	+	-	[Svaba_SR=19,Svaba_PE=21],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=11]	lumpy,svaba,manta	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=KLHL22;DisruptR=CCDC74BP1;Fusion=CCDC74BP1+KLHL22;ClosestL=RNY1P9;ClosestR=MED15	23763093	23763093	17,20476962,20591961	0,0,0
chr22	23936453	23936454	chr22	23946301	23946302	INV	NA	-	-	[Svaba_SR=19,Svaba_PE=15]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=;ClosestL=AP000350.1;ClosestR=AP000350.1	23763094	23763094	16,23936454,23946300	0,0,0
chr22	23943022	23943023	chr22	23949661	23949662	DEL	NA	+	-	[Svaba_SR=14,Svaba_PE=20]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=AP000350.1;ClosestR=AP000350.3	23763094	23763094	15,23943023,23949660	0,0,0
chr22	25537886	25537887	chr22	25554448	25554449	DUP	NA	-	+	[Svaba_SR=2,Svaba_PE=2],[Lumpy_PE=5,Lumpy_SR=1]	lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=CRYBB2P1;ClosestR=AL022329.1	23763094	23763094	3,25537888,25554450	0,0,0
chr22	29187777	29187778	chr22	29344659	29344660	DUP	NA	-	+	[Svaba_SR=31,Svaba_PE=47],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=41,Lumpy_SR=10]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=EWSR1|Tier1;DisruptL=;DisruptR=AP1B1;ClosestL=RNU6-1219P;ClosestR=MIR3653	29406094	29406094	23,29187768,29344661	0,0,0
chr22	29285161	29285162	chr22	29286804	29286805	INV	NA	+	+	[Svaba_SR=17,Svaba_PE=17],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=9]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=EWSR1|Tier1;DisruptL=EWSR1;DisruptR=EWSR1;ClosestL=RHBDD3;ClosestR=RHBDD3	29406094	29406094	10,29285160,29286806	0,0,0
chr22	32501242	32501243	chr22	32501764	32501765	DEL	NA	+	-	[Svaba_SR=4,Svaba_PE=0]	svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;ClosestL=FBXO7;ClosestR=FBXO7	29406279	29406279	3,32501221,32501763	0,0,0
chr22	46073953	46073954	chr22	46234169	46234170	DUP	NA	-	+	[Svaba_SR=75,Svaba_PE=92],[Manta_PE=0,Manta_SR=0],[Lumpy_PE=74,Lumpy_SR=37]	manta,lumpy,svaba	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=MIRLET7BHG;DisruptR=PPARA;Fusion=PPARA+MIRLET7BHG;ClosestL=AL121672.2;ClosestR=CDPF1	46073919	46234134	47,46073952,46234171	0,0,0