#INFO: 1000G => 1000 Genomes Project call set
#INFO: DGV => Database of Genomic Variants
#INFO: COSMIC => COSMIC v86
#INFO: Cancer_census => Cancer Census COSMIC v86
#chr	start	end	type	log2	tool	tumor--normal	info	focal	cytoband
chrX	10446	27188581	DEL	-1.35303873659663	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=P2RY8,CRLF2,ZRSR2,EIF1AX;DisruptL=;DisruptR=AC107419.1	no	chrXp22.33-p21.3
chrX	27188582	52040691	DEL	-0.435692503104429	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=ARAF,SSX1,WAS,FAM47C,BCOR,DDX3X,SSX4,GATA1,TFE3,KDM6A,RBM10;DisruptL=AC107419.1;DisruptR=	no	chrXp21.3-p11.22
chrX	52040692	53249008	DUP	0.530755818673778	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=SSX2,KDM5C;DisruptL=;DisruptR=IQSEC2	yes	chrXp11.22
chrX	53249009	94069000	NEU	0.164612688289862	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=FOXO4,ZMYM3,NONO,SMC1A,AMER1,MSN,MED12,AR,ATRX;DisruptL=IQSEC2;DisruptR=	no	chrXp11.22-q21.32
chrX	94069001	123576326	DUP	0.548557157569587	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=IRS4,BTK,SEPT6;DisruptL=;DisruptR=	no	chrXq21.32-q25
chrX	123576327	156030795	DEL	-0.392080824315164	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=DCAF12L2,RPL10,MTCP1,STAG2,ELF4,PHF6,ATP2B3,FLNA,GPC3,BCORL1;DisruptL=;DisruptR=	no	chrXq25-q28
chr1	791595	11071409	NEU	0.188762065124902	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=TNFRSF14,SKI,RPL22,PRDM16,CAMTA1;DisruptL=AL669831.3,AL669831.5;DisruptR=AL109811.1,EXOSC10	yes	chr1p36.33-p36.22
chr1	11071410	30937957	DEL	-0.384626920644081	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=ID3,MDS2,CASP9,PAX7,MTOR,PRDM2,SPEN,SDHB,ARHGEF10L,ARID1A;DisruptL=AL109811.1,EXOSC10;DisruptR=PUM1	yes	chr1p36.22-p35.2
chr1	30937958	31089319	DUP	1.58807749914621	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=DGV;COSMIC;DisruptL=PUM1;DisruptR=	yes	chr1p35.2
chr1	31089320	83995849	DUP	0.619945183431406	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=MYCL,TAL1,JUN,LCK,SFPQ,THRAP3,CSF3R,MPL,MUTYH,STIL,CDKN2C,FUBP1,JAK1,EPS15;DisruptL=;DisruptR=TTLL7	no	chr1p35.2-p31.1
chr1	83995850	97547226	DEL	-0.347811449372768	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=BCL10,RPL5;DisruptL=TTLL7;DisruptR=DPYD	yes	chr1p31.1-p21.3
chr1	97547227	114928001	DEL	-1.33877721759023	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=RBM15,NRAS,TRIM33;DisruptL=DPYD;DisruptR=SYCP1	yes	chr1p21.3-p13.2
chr1	114928002	117039359	NEU	0.195015995478276	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=ATP1A1;DisruptL=SYCP1;DisruptR=AL445231.1	yes	chr1p13.2-p13.1
chr1	117039360	122510058	DUP	0.674684240909012	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=FAM46C,NOTCH2;DisruptL=AL445231.1;DisruptR=	yes	chr1p13.1-p11.1
chr1	143268055	152269317	DUP	1.55865198227616	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=MLLT11,BCL9,ARNT,PDE4DIP;DisruptL=;DisruptR=FLG-AS1	yes	chr1q21.1-q21.3
chr1	152269318	248946322	DUP	0.514817444172288	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=S100A7,SLC45A3,TPM3,LMNA,PRCC,NTRK1,FCRL4,FCGR2B,DDR2,PRRX1,ABL2,TPR,ELF3,MDM4,ELK4,H3F3A,FH,SDHC,CDC73,PTPRC,AKT3,MUC1,PBX1,RGS7;DisruptL=FLG-AS1;DisruptR=	no	chr1q21.3-q44
chr2	10005	11340510	NEU	0.163277086750744	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=ROCK2	yes	chr2p25.3-p25.1
chr2	11340511	32953080	DEL	-0.38462819244083	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=MYCN,C2orf44,NCOA1,ASXL2,DNMT3A,ALK,BIRC6;DisruptL=ROCK2;DisruptR=LTBP1	no	chr2p25.1-p22.3
chr2	32953081	33018157	DEL	-6.98778118297965	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=LTBP1;DisruptR=LTBP1	yes	chr2p22.3
chr2	33018158	53970146	DEL	-0.369455385095228	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SIX2,EPAS1,MSH6,FBXO11,STRN,EML4,MSH2;DisruptL=LTBP1;DisruptR=PSME4	no	chr2p22.3-p16.2
chr2	53970147	55078446	DEL	-1.34357848195165	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=DGV;COSMIC;DisruptL=PSME4;DisruptR=RTN4	yes	chr2p16.2-p16.1
chr2	55078447	66780763	DEL	-0.360042631236813	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=BCL11A,REL,XPO1;DisruptL=RTN4;DisruptR=	yes	chr2p16.1-p14
chr2	66780764	67038351	DEL	-1.40949760707	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=	yes	chr2p14
chr2	67038352	69932249	DEL	-0.373262019367041	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=MXD1	yes	chr2p14-p13.3
chr2	69932250	70131214	DEL	-1.32167079217216	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=PCBP1;DisruptL=MXD1;DisruptR=	yes	chr2p13.3
chr2	70131215	165996671	DEL	-0.36521636817236	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=CXCR4,DCTN1,TMEM127,RANBP2,ACVR1,RGPD3,ERCC3,AFF3,PAX8,LRP1B,ACVR2A;DisruptL=;DisruptR=AC010127.1,SCN1A	no	chr2p13.3-q24.3
chr2	165996672	166087601	DEL	-7.42732232500826	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=AC010127.1,SCN1A;DisruptR=AC010127.1,SCN1A	yes	chr2q24.3
chr2	166087602	221633776	DEL	-0.349941041341045	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=HOXD13,HOXD11,FEV,NFE2L2,CASP8,CD28,CREB1,IDH1,BARD1,ATIC,COL3A1,SF3B1,ITGAV,PMS1,ERBB4;DisruptL=AC010127.1,SCN1A;DisruptR=	no	chr2q24.3-q36.1
chr2	221633777	222260575	NEU	0.199741295695565	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=PAX3;DisruptL=;DisruptR=PAX3	yes	chr2q36.1
chr2	222260576	242183395	DEL	-0.376346270593041	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=ACKR3,ACSL3,CUL3,PAX3;DisruptL=PAX3;DisruptR=	yes	chr2q36.1-q37.3
chr3	10005	9464867	DEL	-0.383111795818861	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SRGAP3;DisruptL=;DisruptR=SETD5	yes	chr3p26.3-p25.3
chr3	9464868	10565855	NEU	0.194227378078585	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=VHL,FANCD2;DisruptL=SETD5;DisruptR=ATP2B2	yes	chr3p25.3
chr3	10565856	57140872	DEL	-0.382195300302721	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=CCR4,MYD88,BAP1,PPARG,RAF1,MLH1,CTNNB1,NCKIPSD,RHOA,XPC,TGFBR2,SETD2,PBRM1,CACNA1D,FBLN2;DisruptL=ATP2B2;DisruptR=IL17RD	no	chr3p25.3-p14.3
chr3	57140873	57246745	DUP	0.648629878544429	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=IL17RD;DisruptR=APPL1	yes	chr3p14.3
chr3	57246746	65203241	DEL	-0.4003593778066	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=FHIT;DisruptL=APPL1;DisruptR=	yes	chr3p14.3-p14.1
chr3	65203242	65229048	DEL	-6.57221290304305	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=LINC02040	yes	chr3p14.1
chr3	65229049	129572682	DEL	-0.37728540194436	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=MITF,TFG,GATA2,RPN1,CNBP,FOXP1,CBLB,POLQ,ROBO2,EPHA3;DisruptL=;DisruptR=PLXND1	no	chr3p14.1-q22.1
chr3	129572683	129700971	DUP	0.619559649945551	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=PLXND1;DisruptR=TMCC1	yes	chr3q22.1
chr3	129700972	198139690	DEL	-0.368222862325226	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=FOXL2,SOX2,EIF4A2,GMPS,MECOM,TBL1XR1,PIK3CA,ETV5,BCL6,MUC4,TFRC,STAG1,PIK3CB,ATR,WWTR1,MLF1,MAP3K13,IGF2BP2,MB21D2,LPP,TP63;DisruptL=TMCC1;DisruptR=	no	chr3q22.1-q29
chr4	10011	2795619	NEU	0.0905055831550929	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=FGFR3,WHSC1;DisruptL=;DisruptR=SH3BP2	yes	chr4p16.3
chr4	2795620	13433766	DEL	-0.503159553709621	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=SH3BP2;DisruptR=RAB28	yes	chr4p16.3-p15.33
chr4	13433767	13867711	NEU	0.12488339096113	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=RAB28;DisruptR=LINC01182	yes	chr4p15.33
chr4	13867712	136871289	DEL	-0.367166321427136	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=RHOH,SLC34A2,PHOX2B,TEC,FIP1L1,CHIC2,KIT,KDR,IL2,N4BP2,PDGFRA,PTPN13,RAP1GDS1,TET2,LEF1,FAT4,AFF1;DisruptL=LINC01182;DisruptR=LINC02511	no	chr4p15.33-q28.3
chr4	136871290	136898089	DEL	-7.89537659437336	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=LINC02511;DisruptR=LINC02511	yes	chr4q28.3
chr4	136898090	145157668	DEL	-0.348831589739634	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=LINC02511;DisruptR=OTUD4	yes	chr4q28.3-q31.21
chr4	145157669	145584968	DUP	0.709865530426138	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=OTUD4;DisruptR=	yes	chr4q31.21
chr4	145584969	190066290	DEL	-0.357560952215696	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=FBXW7,CASP3,FAT1;DisruptL=;DisruptR=DBET	no	chr4q31.21-q35.2
chr5	11484	46492487	DUP	0.20224924633789	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SDHA,TERT,IL7R,LIFR,CDH10,CTNND2,DROSHA;DisruptL=;DisruptR=	no	chr5p15.33-p11
chr5	46492488	181449255	DEL	-0.341604099206634	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=RAD17,MAP3K1,APC,PDGFRB,CD74,ITK,PWWP2A,NPM1,FGFR4,IL6ST,PIK3R1,ACSL6,AFF4,ARHGAP26,CSF1R,EBF1,TLX3,FLT4,NSD1;DisruptL=;DisruptR=	no	chr5p11-q35.3
chr6	89830	1864356	DUP	0.55527066916715	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=IRF4;DisruptL=;DisruptR=GMDS	yes	chr6p25.3
chr6	1864357	5740655	DUP	0.209170939022053	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=GMDS;DisruptR=FARS2	yes	chr6p25.3-p25.1
chr6	5740656	41330045	DUP	0.631375050114868	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=HIST1H3B,HIST1H4I,HLA-A,POU5F1,DAXX,CDKN1A,PIM1,DEK,TRIM27,HMGA1,FANCE,SRSF3;DisruptL=FARS2;DisruptR=	no	chr6p25.1-p21.1
chr6	41330046	42280534	DUP	1.52834815539619	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=TFEB,CCND3;DisruptL=;DisruptR=TRERF1	yes	chr6p21.1
chr6	42280535	78257462	DEL	-0.360687477471498	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=NFKBIE,HSP90AB1,BMP5;DisruptL=TRERF1;DisruptR=	no	chr6p21.1-q14.1
chr6	78257463	78326601	DEL	-7.48713731126922	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr6q14.1
chr6	78326602	134006347	DEL	-0.358305608401172	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=PRDM1,CCNC,FOXO3,ROS1,GOPC,RSPO3,PTPRK,EPHA7;DisruptL=;DisruptR=SLC2A12	no	chr6q14.1-q23.2
chr6	134006348	134216592	DEL	-7.1017137461506	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SGK1;DisruptL=SLC2A12;DisruptR=SGK1	yes	chr6q23.2
chr6	134216593	149186361	DEL	-0.338883287315301	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=MYB,BCLAF1,TNFAIP3,ECT2L;DisruptL=SGK1;DisruptR=	yes	chr6q23.2-q25.1
chr6	149186362	149656200	DUP	0.326957912170386	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=	yes	chr6q25.1
chr6	149656201	170740360	DEL	-0.392216825978375	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=EZR,FGFR1OP,ARID1B,QKI,MLLT4,ESR1;DisruptL=;DisruptR=	no	chr6q25.1-q27
chr7	16339	149535564	DUP	0.611761376707665	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=HOXA11,HOXA13,CARD11,PMS2,RAC1,ETV1,HNRNPA2B1,HOXA9,FKBP9,SFRP4,ZNF479,SBDS,POT1,SMO,KIAA1549,FAM131B,EZH2,JAZF1,EGFR,ELN,HIP1,GRM3,AKAP9,CDK6,TRRAP,CUX1,MET,CREB3L2,TRIM24,BRAF,SND1,CNTNAP2,IKZF1;DisruptL=AC215522.3;DisruptR=	no	chr7p22.3-q36.1
chr7	149535565	159335873	DEL	-0.412384298761612	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=MNX1,KMT2C;DisruptL=;DisruptR=	yes	chr7q36.1-q36.3
chr8	71162	101318335	NEU	0.18616113812467	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=TCEA1,PLAG1,CHCHD7,HEY1,COX6C,ARHGEF10,LEPROTL1,WHSC1L1,FGFR1,IKBKB,NBN,CDH17,PABPC1,PCM1,WRN,NRG1,ANK1,NCOA2,RUNX1T1,HOOK3,PREX2,CNBD1;DisruptL=;DisruptR=	no	chr8p23.3-q22.3
chr8	101318336	101478031	DUP	0.912960075923799	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=AP001207.3	yes	chr8q22.3
chr8	101478032	123656900	DUP	0.208257861253759	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=EIF3E,RAD21,UBR5,EXT1,RSPO2,CSMD3;DisruptL=AP001207.3;DisruptR=AC090193.1	no	chr8q22.3-q24.13
chr8	123656901	126449871	DEL	-1.33321098130751	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=AC090193.1;DisruptR=	yes	chr8q24.13-q24.21
chr8	126449872	128452816	DUP	0.351168673059242	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=MYC;DisruptL=;DisruptR=LINC00824	yes	chr8q24.21
chr8	128458951	142901153	NEU	0.138839796581854	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=NDRG1,FAM135B;DisruptL=LINC00824;DisruptR=GML	yes	chr8q24.21-q24.3
chr8	142901154	145078494	DUP	0.89479310347083	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=RECQL4;DisruptL=GML;DisruptR=	yes	chr8q24.3
chr9	10000	12889208	NEU	0.190559220338517	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=CD274,PDCD1LG2,JAK2,PTPRD;DisruptL=;DisruptR=	yes	chr9p24.3-p23
chr9	12889209	13056039	DUP	1.24446834345993	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=;DisruptR=	yes	chr9p23
chr9	13056040	112114443	NEU	0.174831507754352	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=OMD,KLF4,TAL2,PSIP1,CDKN2A,FANCG,SYK,PTCH1,XPA,NR4A3,NFIB,MLLT3,PAX5,GNAQ,WNK2,FANCC;DisruptL=;DisruptR=SUSD1	no	chr9p23-q32
chr9	112114444	112332600	DUP	0.984854978397939	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;DisruptL=SUSD1;DisruptR=PTBP3	yes	chr9q32
chr9	112332601	138313848	NEU	0.159165658894365	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SET,ABL1,RALGDS,BRD3,NOTCH1,TNC,CNTRL,PPP6C,NUP214,TSC1,FNBP1;DisruptL=PTBP3;DisruptR=	no	chr9q32-q34.3
chr10	10287	1138117	DUP	0.885438147437988	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=LARP4B;DisruptL=;DisruptR=	yes	chr10p15.3
chr10	1138118	1549130	NEU	0.101478984097132	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=DGV;COSMIC;DisruptL=;DisruptR=ADARB2-AS1,ADARB2	yes	chr10p15.3
chr10	1549131	22502452	DUP	0.902443421333137	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=KLF6,GATA3,MLLT10;DisruptL=ADARB2-AS1,ADARB2;DisruptR=	no	chr10p15.3-p12.2
chr10	22502453	71741418	DUP	0.217123693228152	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=NCOA4,ABI1,KIF5B,PRF1,RET,A1CF,CCDC6,TET1,ZEB1;DisruptL=;DisruptR=CDH23	no	chr10p12.2-q22.1
chr10	71741419	77999458	DUP	0.643206847473894	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=KAT6B;DisruptL=CDH23;DisruptR=POLR3A	yes	chr10q22.1-q22.3
chr10	77999459	82676186	DUP	1.21355728144028	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=NUTM2B;DisruptL=POLR3A;DisruptR=NRG3	yes	chr10q22.3-q23.1
chr10	82676187	133787316	DEL	-0.396985193032948	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=TLX1,NUTM2A,CYP2C8,NFKB2,BMPR1A,PTEN,FAS,CPEB3,SUFU,NT5C2,VTI1A,TCF7L2,KIAA1598,FGFR2,MGMT;DisruptL=NRG3;DisruptR=	no	chr10q23.1-q26.3
chr11	128355	5558211	DEL	-0.648010315002946	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=HRAS,NUP98,CARS;DisruptL=LINC01001;DisruptR=OR52B5P,AC104389.4	yes	chr11p15.5-p15.4
chr11	5558212	9130419	DUP	0.307411822838939	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=LMO1;DisruptL=OR52B5P,AC104389.4;DisruptR=SCUBE2	yes	chr11p15.4
chr11	9130420	10460500	NEU	-0.058679010765948	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=SCUBE2;DisruptR=AMPD3	yes	chr11p15.4
chr11	10460501	78421457	DUP	0.317837832417355	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=MYOD1,FANCF,CLP1,FEN1,MEN1,MALAT1,WT1,LMO2,CREB3L1,DDB2,SDHAF2,CCND1,NUMA1,EXT2,CTNND1;DisruptL=AMPD3;DisruptR=AP003086.2	no	chr11p15.4-q14.1
chr11	78421458	90936582	DEL	-0.630057267094264	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=EED,PICALM;DisruptL=AP003086.2;DisruptR=	yes	chr11q14.1-q14.3
chr11	90936583	135076522	DUP	0.30464351411693	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SDHD,KCNJ5,FAT3,BIRC3,POU2AF1,PAFAH1B2,DDX6,BCL9L,FOXR1,MAML2,ATM,DDX10,ZBTB16,CBL,ARHGEF12,FLI1,KMT2A;DisruptL=;DisruptR=	no	chr11q14.3-q25
chr12	41087	28617172	DUP	0.576816326065555	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=PTPN6,CDKN1B,KDM5A,CCND2,CHD4,ZNF384,KRAS,ETV6,ETNK1,PPFIBP1,ERC1;DisruptL=;DisruptR=	no	chr12p13.33-p11.22
chr12	28617173	128424612	DEL	-0.366059277417124	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=HOXC13,HOXC11,NAB2,GLI1,DDIT3,CDK4,BTG1,TBX3,SETD1B,COL2A1,KMT2D,PRPF40B,SMARCD1,ATF1,NACA,STAT6,LRIG3,WIF1,PTPRB,USP44,SH2B3,ZCCHC8,ARID2,ERBB3,HMGA2,MDM2,CHST11,ALDH2,PTPN11,HNF1A,BCL7A,CLIP1,NCOR2;DisruptL=;DisruptR=TMEM132C	no	chr12p11.22-q24.32
chr12	128424613	129071365	DEL	-1.41907238630741	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=TMEM132C;DisruptR=	yes	chr12q24.32-q24.33
chr12	129071366	131245724	DEL	-0.442426323980279	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=	yes	chr12q24.33
chr12	131245725	131344272	DEL	-3.64012593443036	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=DGV,1000G;COSMIC;DisruptL=;DisruptR=	yes	chr12q24.33
chr12	131344273	133264924	DEL	-0.402200856571245	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=POLE;DisruptL=;DisruptR=	yes	chr12q24.33
chr13	16166247	58800227	NEU	-0.0328662949397596	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=CYSLTR2,CDX2,ZNF198,FLT3,BRCA2,LHFP,FOXO1,RB1,NBEA,LCP1;DisruptL=;DisruptR=	no	chr13p11.2-q21.1
chr13	58800228	88970765	DEL	-1.5382001852454	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=	no	chr13q21.1-q31.2
chr13	88970766	102428502	DUP	0.400145099257036	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SOX21,GPC5;DisruptL=;DisruptR=	yes	chr13q31.2-q33.1
chr13	102428503	102801717	DUP	0.981827120660921	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=BIVM,BIVM-ERCC5	yes	chr13q33.1
chr13	102801718	114354111	DUP	0.381900410516164	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=ERCC5;DisruptL=BIVM,BIVM-ERCC5;DisruptR=	yes	chr13q33.1-q34
chr14	18223655	39133588	DEL	-0.56319564052335	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=NKX2-1,FOXA1,CCNB1IP1,ARHGAP5,BAZ1A;DisruptL=;DisruptR=GEMIN2	no	chr14q11.2-q21.1
chr14	39133589	39342722	DUP	0.507473222712137	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=GEMIN2;DisruptR=MIA2	yes	chr14q21.1
chr14	39342723	41140316	DEL	-0.563886937284461	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=MIA2;DisruptR=	yes	chr14q21.1
chr14	41140317	41200380	DEL	-7.67853832914764	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr14q21.1
chr14	41200381	63236251	DEL	-0.5516207125085	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SIX1,NIN,KTN1,HIF1A;DisruptL=;DisruptR=RHOJ	no	chr14q21.1-q23.2
chr14	63236252	63870830	DEL	-7.03569711238507	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=RHOJ;DisruptR=SYNE2	yes	chr14q23.2
chr14	63870831	64117654	DEL	-0.552655616302502	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=SYNE2;DisruptR=ESR2,SYNE2	yes	chr14q23.2
chr14	64117655	64374366	DUP	0.398191387962133	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=ESR2,SYNE2;DisruptR=TEX21P	yes	chr14q23.2-q23.3
chr14	64374367	68301567	DEL	-0.532757010681424	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=MAX,RAD51B,GPHN;DisruptL=TEX21P;DisruptR=RAD51B	yes	chr14q23.3-q24.1
chr14	68301568	68621029	DUP	0.556329896272615	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=RAD51B;DisruptL=RAD51B;DisruptR=RAD51B	yes	chr14q24.1
chr14	68621030	73199736	DEL	-0.549132242262798	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=RAD51B;DisruptR=PSEN1	yes	chr14q24.1-q24.2
chr14	73199737	106883618	NEU	0.00654125964892222	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=TCL1A,DICER1,AKT1,TSHR,TRIP11,GOLGA5,BCL11B,HSP90AA1;DisruptL=PSEN1;DisruptR=	no	chr14q24.2-q32.33
chr15	17000005	34410561	DEL	-0.40746174142996	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=NUTM1;DisruptL=;DisruptR=AC025678.2,GOLGA8A	yes	chr15p11.2-q14
chr15	34410562	34526119	DEL	-6.83973576825344	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=DGV,1000G;COSMIC;DisruptL=AC025678.2,GOLGA8A;DisruptR=GOLGA8B	yes	chr15q14
chr15	34526120	71887858	DEL	-0.3453425835607	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=BUB1B,KNSTRN,B2M,CASC5,USP8,TCF12,MAP2K1,MYO5A,SMAD3;DisruptL=GOLGA8B;DisruptR=MYO9A	no	chr15q14-q23
chr15	71887859	72152243	DEL	-6.88943245593962	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=MYO9A;DisruptR=AC020779.2	yes	chr15q23
chr15	72152244	84936396	DEL	-0.370791297789988	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=PML;DisruptL=AC020779.2;DisruptR=SLC28A1	yes	chr15q23-q25.3
chr15	84936397	85513789	DUP	0.268950038332005	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=SLC28A1;DisruptR=AKAP13	yes	chr15q25.3
chr15	85513790	90138915	DEL	-0.407068723430388	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=POLG,IDH2,NTRK3;DisruptL=AKAP13;DisruptR=	yes	chr15q25.3-q26.1
chr15	90138916	90290294	DUP	0.941083322062214	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=AC091167.6	yes	chr15q26.1
chr15	90290295	101981087	DEL	-0.390401287924206	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=FES,BLM,CRTC3,CHD2;DisruptL=AC091167.6;DisruptR=	yes	chr15q26.1-q26.3
chr16	10005	12896986	DEL	-0.38502089797293	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=TRAF7,SOCS1,RMI2,TNFRSF17,AXIN1,TSC2,RUNDC2A,CREBBP,GRIN2A,CIITA,NTHL1;DisruptL=;DisruptR=	yes	chr16p13.3-p13.12
chr16	12896987	30066716	NEU	0.185658215717701	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=ERCC4,PALB2,IL21R,MYH11,PRKCB;DisruptL=;DisruptR=AC093512.2,ALDOA	yes	chr16p13.12-p11.2
chr16	30066717	90226217	DEL	-0.374313797481476	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=FUS,MAF,CYLD,HERPUD1,CDH11,CBFB,RFWD3,CBFA2T3,CTCF,CDH1,ZFHX3,FANCA;DisruptL=AC093512.2,ALDOA;DisruptR=	no	chr16p11.2-q24.3
chr17	168977	39261864	DEL	-0.377121826442997	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=TP53,YWHAE,USP6,PER1,FLCN,TAF15,MLLT6,LASP1,RABEP1,GAS7,MAP2K4,NCOR1,SPECC1,NF1,SUZ12;DisruptL=DOC2B;DisruptR=FBXL20	no	chr17p13.3-q12
chr17	39261865	39349814	DEL	-6.28646714258283	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=FBXL20;DisruptR=FBXL20	yes	chr17q12
chr17	39349815	83247341	DEL	-0.356274378006704	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=CCR7,H3F3B,SRSF2,CANT1,CDK12,RARA,ETV4,SPOP,RNF43,PPM1D,CD79B,DDX5,PRKAR1A,ASPSCR1,ERBB2,SMARCE1,STAT5B,STAT3,BRCA1,KAT7,COL1A1,HLF,MSI2,CLTC,BRIP1,AXIN2,SEPT9,RNF213;DisruptL=FBXL20;DisruptR=	no	chr17q12-q25.3
chr18	10010	8939025	DUP	0.615449418105386	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=	yes	chr18p11.32-p11.22
chr18	8939026	10814015	DUP	0.947690828664388	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=PIEZO2	yes	chr18p11.22
chr18	10814016	55686228	DUP	0.602142121689207	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=SMAD2,SMAD4,SS18,SETBP1,DCC,ZNF521;DisruptL=PIEZO2;DisruptR=	no	chr18p11.22-q21.2
chr18	55686229	80263172	DEL	-0.404229302135914	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=KDSR,BCL2,MALT1;DisruptL=;DisruptR=	no	chr18q21.2-q23
chr19	90733	5824138	DEL	-0.387196867892613	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=FSTL3,STK11,TCF3,GNA11,MAP2K2,SH3GL1;DisruptL=;DisruptR=NRTN	yes	chr19p13.3
chr19	5824139	37270966	DUP	0.584169789381833	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=CD209,KEAP1,LYL1,CEBPA,MLLT1,MUC16,CALR,PRKACA,DNAJB1,BRD4,TPM4,JAK3,ZNF429,CCNE1,VAV1,DNM2,SMARCA4,ELL,CRTC1,CEP89,LSM14A;DisruptL=NRTN;DisruptR=AC016590.1	no	chr19p13.3-q13.12
chr19	37270967	50944418	NEU	0.133540151653474	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=BCL3,BCL2L12,KLK2,CD79A,CIC,CBLC,ERCC2,BAX,POLD1,AKT2;DisruptL=AC016590.1;DisruptR=KLK5	yes	chr19q13.12-q13.41
chr19	50944419	58607515	DUP	0.539712767376172	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=TFPT,PPP2R1A,ZNF331,CNOT3;DisruptL=KLK5;DisruptR=	yes	chr19q13.41-q13.43
chr20	67260	4273275	DUP	0.59160050486813	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SIRPA;DisruptL=;DisruptR=	yes	chr20p13
chr20	4273276	6218512	DUP	0.930624664121186	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;DisruptL=;DisruptR=	yes	chr20p13-p12.3
chr20	6218513	32713333	DUP	0.605349987390186	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;Cancer_census=CRNKL1,ASXL1;DisruptL=;DisruptR=COMMD7,FO393400.1	no	chr20p12.3-q11.21
chr20	32713334	64334067	DEL	-0.392073325183698	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=MAFB,SRC,TOP1,SDC4,SALL4,GNAS,SS18L1,PTK6,PLCG1,NFATC2,PTPRT;DisruptL=COMMD7,FO393400.1;DisruptR=	no	chr20q11.21-q13.33
chr21	13044018	46699872	NEU	0.197103243052255	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=OLIG2,TMPRSS2,U2AF1,RUNX1,ERG;DisruptL=ANKRD30BP2;DisruptR=	no	chr21q11.2-q22.3
chr22	10514978	50807810	DEL	-0.394644399700188	bicseq2	HCC1187-NovaSeq--HCC-1187BL-NovaSeq	known=;COSMIC;Cancer_census=SEPT5,APOBEC3B,DGCR8,LZTR1,MAPK1,SMARCB1,ZNRF3,EWSR1,ZNF278,ISX,PDGFB,MKL1,CLTCL1,BCR,MN1,CHEK2,NF2,MYH9,EP300;DisruptL=;DisruptR=	no	chr22p11.2-q13.33