#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	27188681	DEL	-1.35681330788642	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=P2RY8|Tier1,CRLF2|Tier1,ZRSR2|Tier1,EIF1AX|Tier2;DisruptL=;DisruptR=AC107419.1	no	chrXp22.33-p21.3
chrX	27188682	52040591	DEL	-0.436172177571252	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=ARAF|Tier2,SSX1|Tier1,WAS|Tier1,FAM47C|Tier2,BCOR|Tier1,DDX3X|Tier1,SSX4|Tier1,GATA1|Tier1,TFE3|Tier1,KDM6A|Tier1,RBM10|Tier1;DisruptL=AC107419.1;DisruptR=	no	chrXp21.3-p11.22
chrX	52040592	53248308	DUP	0.527216866715165	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=SSX2|Tier1,KDM5C|Tier1;DisruptL=;DisruptR=IQSEC2	yes	chrXp11.22
chrX	53248309	94069100	NEU	0.164614483451888	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=FOXO4|Tier1,ZMYM3|Tier2,NONO|Tier1,SMC1A|Tier2,AMER1|Tier1,MSN|Tier1,MED12|Tier1,AR|Tier1,ATRX|Tier1;DisruptL=IQSEC2;DisruptR=	no	chrXp11.22-q21.32
chrX	94069101	123576326	DUP	0.548577997423895	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=IRS4|Tier1,BTK|Tier1,SEPT6|Tier2;DisruptL=;DisruptR=	no	chrXq21.32-q25
chrX	123576327	156030795	DEL	-0.393895581922145	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=DCAF12L2|Tier2,RPL10|Tier1,MTCP1|Tier1,STAG2|Tier1,ELF4|Tier1,PHF6|Tier1,ATP2B3|Tier1,FLNA|Tier2,GPC3|Tier1,BCORL1|Tier1;DisruptL=;DisruptR=	no	chrXq25-q28
chr1	791595	11072009	NEU	0.191786392207508	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=TNFRSF14|Tier1,SKI|Tier2,RPL22|Tier1,PRDM16|Tier1,CAMTA1|Tier1;DisruptL=AL669831.3,AL669831.5;DisruptR=AL109811.1,EXOSC10	yes	chr1p36.33-p36.22
chr1	11072010	30937957	DEL	-0.379943842740553	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=ID3|Tier2,MDS2|Tier2,CASP9|Tier2,PAX7|Tier1,MTOR|Tier1,PRDM2|Tier2,SPEN|Tier1,SDHB|Tier1,ARHGEF10L|Tier2,ARID1A|Tier1;DisruptL=AL109811.1,EXOSC10;DisruptR=PUM1	yes	chr1p36.22-p35.2
chr1	30937958	31088919	DUP	1.56603314261963	bicseq2	HCC1187_80--HCC-1187BL_40	known=DGV;COSMIC;DisruptL=PUM1;DisruptR=	yes	chr1p35.2
chr1	31088920	83995849	DUP	0.621926897648759	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=MYCL|Tier1,TAL1|Tier1,JUN|Tier1,LCK|Tier1,SFPQ|Tier1,THRAP3|Tier2,CSF3R|Tier1,MPL|Tier1,MUTYH|Tier1,STIL|Tier1,CDKN2C|Tier1,FUBP1|Tier1,JAK1|Tier1,EPS15|Tier1;DisruptL=;DisruptR=TTLL7	no	chr1p35.2-p31.1
chr1	83995850	97547226	DEL	-0.348091643348319	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=BCL10|Tier1,RPL5|Tier1;DisruptL=TTLL7;DisruptR=DPYD	yes	chr1p31.1-p21.3
chr1	97547227	114927901	DEL	-1.34736101936707	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=RBM15|Tier1,NRAS|Tier1,TRIM33|Tier1;DisruptL=DPYD;DisruptR=SYCP1	yes	chr1p21.3-p13.2
chr1	114927902	117039159	DUP	0.204819487156242	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=ATP1A1|Tier1;DisruptL=SYCP1;DisruptR=AL445231.1	yes	chr1p13.2-p13.1
chr1	117039160	122510058	DUP	0.678379722849264	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=FAM46C|Tier1,NOTCH2|Tier1;DisruptL=AL445231.1;DisruptR=	yes	chr1p13.1-p11.1
chr1	143268055	152269317	DUP	1.56235318819067	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=MLLT11|Tier1,BCL9|Tier1,ARNT|Tier1,PDE4DIP|Tier1;DisruptL=;DisruptR=FLG-AS1	yes	chr1q21.1-q21.3
chr1	152269318	248946322	DUP	0.517757761931357	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=S100A7|Tier2,SLC45A3|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,FH|Tier1,SDHC|Tier1,CDC73|Tier1,PTPRC|Tier1,AKT3|Tier2,MUC1|Tier1,PBX1|Tier1,RGS7|Tier2;DisruptL=FLG-AS1;DisruptR=	no	chr1q21.3-q44
chr2	10005	11340610	NEU	0.167885676498243	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=;DisruptR=ROCK2	yes	chr2p25.3-p25.1
chr2	11340611	32953080	DEL	-0.382612038343206	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=MYCN|Tier1,C2orf44|Tier1,NCOA1|Tier1,ASXL2|Tier2,DNMT3A|Tier1,ALK|Tier1,BIRC6|Tier2;DisruptL=ROCK2;DisruptR=LTBP1	no	chr2p25.1-p22.3
chr2	32953081	33018157	DEL	-7.63347481833913	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=LTBP1;DisruptR=LTBP1	yes	chr2p22.3
chr2	33018158	53970246	DEL	-0.370090413460723	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=SIX2|Tier2,EPAS1|Tier1,MSH6|Tier1,FBXO11|Tier1,STRN|Tier1,EML4|Tier1,MSH2|Tier1;DisruptL=LTBP1;DisruptR=PSME4	no	chr2p22.3-p16.2
chr2	53970247	55078446	DEL	-1.32859230532598	bicseq2	HCC1187_80--HCC-1187BL_40	known=DGV;COSMIC;DisruptL=PSME4;DisruptR=RTN4	yes	chr2p16.2-p16.1
chr2	55078447	66780863	DEL	-0.361838706381313	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=BCL11A|Tier1,REL|Tier1,XPO1|Tier1;DisruptL=RTN4;DisruptR=	yes	chr2p16.1-p14
chr2	66780864	67038351	DEL	-1.39151558831877	bicseq2	HCC1187_80--HCC-1187BL_40	known=;DisruptL=;DisruptR=	yes	chr2p14
chr2	67038352	165996671	DEL	-0.368338819878283	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=PCBP1|Tier2,CXCR4|Tier1,DCTN1|Tier1,TMEM127|Tier1,RANBP2|Tier1,ACVR1|Tier1,RGPD3|Tier2,ERCC3|Tier1,AFF3|Tier1,PAX8|Tier1,LRP1B|Tier1,ACVR2A|Tier1;DisruptL=;DisruptR=AC010127.1,SCN1A	no	chr2p14-q24.3
chr2	165996672	166087601	DEL	-8.19124861734876	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=AC010127.1,SCN1A;DisruptR=AC010127.1,SCN1A	yes	chr2q24.3
chr2	166087602	221633776	DEL	-0.352938128167212	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=HOXD13|Tier1,HOXD11|Tier1,FEV|Tier1,NFE2L2|Tier1,CASP8|Tier1,CD28|Tier2,CREB1|Tier1,IDH1|Tier1,BARD1|Tier1,ATIC|Tier1,COL3A1|Tier2,SF3B1|Tier1,ITGAV|Tier2,PMS1|Tier2,ERBB4|Tier1;DisruptL=AC010127.1,SCN1A;DisruptR=	no	chr2q24.3-q36.1
chr2	221633777	222290575	NEU	0.198083148394996	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=PAX3|Tier1;DisruptL=;DisruptR=PAX3	yes	chr2q36.1
chr2	222290576	242183395	DEL	-0.375776856538659	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=ACKR3|Tier1,ACSL3|Tier1,CUL3|Tier2,PAX3|Tier1;DisruptL=PAX3;DisruptR=	yes	chr2q36.1-q37.3
chr3	10005	9464867	DEL	-0.386655589234064	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=SRGAP3|Tier2;DisruptL=;DisruptR=SETD5	yes	chr3p26.3-p25.3
chr3	9464868	10566055	NEU	0.195663868007105	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=VHL|Tier1,FANCD2|Tier1;DisruptL=SETD5;DisruptR=ATP2B2	yes	chr3p25.3
chr3	10566056	129572182	DEL	-0.3802654855062	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=CCR4|Tier2,MYD88|Tier1,BAP1|Tier1,PPARG|Tier1,RAF1|Tier1,MLH1|Tier1,CTNNB1|Tier1,NCKIPSD|Tier2,RHOA|Tier1,MITF|Tier1,TFG|Tier1,GATA2|Tier1,RPN1|Tier1,CNBP|Tier1,XPC|Tier1,TGFBR2|Tier1,SETD2|Tier1,PBRM1|Tier1,CACNA1D|Tier1,FOXP1|Tier1,CBLB|Tier1,POLQ|Tier1,FBLN2|Tier2,FHIT|Tier1,ROBO2|Tier2,EPHA3|Tier2;DisruptL=ATP2B2;DisruptR=PLXND1	no	chr3p25.3-q22.1
chr3	129572183	129701071	DUP	0.623449917802003	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=PLXND1;DisruptR=TMCC1	yes	chr3q22.1
chr3	129701072	198139690	DEL	-0.368714335248503	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=FOXL2|Tier1,SOX2|Tier1,EIF4A2|Tier1,GMPS|Tier2,MECOM|Tier1,TBL1XR1|Tier1,PIK3CA|Tier1,ETV5|Tier1,BCL6|Tier1,MUC4|Tier2,TFRC|Tier2,STAG1|Tier2,PIK3CB|Tier1,ATR|Tier1,WWTR1|Tier1,MLF1|Tier1,MAP3K13|Tier1,IGF2BP2|Tier2,MB21D2|Tier2,LPP|Tier1,TP63|Tier1;DisruptL=TMCC1;DisruptR=	no	chr3q22.1-q29
chr4	10011	2795619	NEU	0.0954156839883709	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=FGFR3|Tier1,WHSC1|Tier1;DisruptL=;DisruptR=SH3BP2	yes	chr4p16.3
chr4	2795620	13433766	DEL	-0.500789469868394	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=SH3BP2;DisruptR=RAB28	yes	chr4p16.3-p15.33
chr4	13433767	13868011	NEU	0.131374353999378	bicseq2	HCC1187_80--HCC-1187BL_40	known=;DisruptL=RAB28;DisruptR=LINC01182	yes	chr4p15.33
chr4	13868012	136871289	DEL	-0.368558978579993	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=RHOH|Tier1,SLC34A2|Tier1,PHOX2B|Tier1,TEC|Tier2,FIP1L1|Tier1,CHIC2|Tier2,KIT|Tier1,KDR|Tier1,IL2|Tier1,N4BP2|Tier2,PDGFRA|Tier1,PTPN13|Tier1,RAP1GDS1|Tier1,TET2|Tier1,LEF1|Tier1,FAT4|Tier1,AFF1|Tier1;DisruptL=LINC01182;DisruptR=LINC02511	no	chr4p15.33-q28.3
chr4	136871290	136898089	DEL	-8.13820617629615	bicseq2	HCC1187_80--HCC-1187BL_40	known=;DisruptL=LINC02511;DisruptR=LINC02511	yes	chr4q28.3
chr4	136898090	145157668	DEL	-0.348595078886939	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=LINC02511;DisruptR=OTUD4	yes	chr4q28.3-q31.21
chr4	145157669	145584968	DUP	0.710825124489423	bicseq2	HCC1187_80--HCC-1187BL_40	known=;DisruptL=OTUD4;DisruptR=	yes	chr4q31.21
chr4	145584969	190066290	DEL	-0.358142908258927	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=FBXW7|Tier1,CASP3|Tier2,FAT1|Tier1;DisruptL=;DisruptR=DBET	no	chr4q31.21-q35.2
chr5	11484	46502194	DUP	0.201712038158966	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=SDHA|Tier1,TERT|Tier1,IL7R|Tier1,LIFR|Tier1,CDH10|Tier2,CTNND2|Tier2,DROSHA|Tier1;DisruptL=;DisruptR=	no	chr5p15.33-p11
chr5	46502195	181449255	DEL	-0.343587656036894	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=RAD17|Tier2,MAP3K1|Tier1,APC|Tier1,PDGFRB|Tier1,CD74|Tier1,ITK|Tier1,PWWP2A|Tier2,NPM1|Tier1,FGFR4|Tier1,IL6ST|Tier1,PIK3R1|Tier1,ACSL6|Tier2,AFF4|Tier1,ARHGAP26|Tier1,CSF1R|Tier2,EBF1|Tier1,TLX3|Tier1,FLT4|Tier1,NSD1|Tier1;DisruptL=;DisruptR=	no	chr5p11-q35.3
chr6	89830	1864356	DUP	0.568469505382624	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=IRF4|Tier1;DisruptL=;DisruptR=GMDS	yes	chr6p25.3
chr6	1864357	5740655	DUP	0.214571277845255	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=GMDS;DisruptR=FARS2	yes	chr6p25.3-p25.1
chr6	5740656	41330045	DUP	0.633866903034582	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=HIST1H3B|Tier1,HIST1H4I|Tier1,HLA-A|Tier1,POU5F1|Tier1,DAXX|Tier1,CDKN1A|Tier2,PIM1|Tier1,DEK|Tier1,TRIM27|Tier1,HMGA1|Tier1,FANCE|Tier1,SRSF3|Tier1;DisruptL=FARS2;DisruptR=	no	chr6p25.1-p21.1
chr6	41330046	42280534	DUP	1.53520666933242	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=TFEB|Tier1,CCND3|Tier1;DisruptL=;DisruptR=TRERF1	yes	chr6p21.1
chr6	42280535	78257462	DEL	-0.362193138055302	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=NFKBIE|Tier1,HSP90AB1|Tier1,BMP5|Tier2;DisruptL=TRERF1;DisruptR=	no	chr6p21.1-q14.1
chr6	78257463	78326601	DEL	-7.49425797379239	bicseq2	HCC1187_80--HCC-1187BL_40	known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr6q14.1
chr6	78326602	134006347	DEL	-0.360487340931412	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=PRDM1|Tier1,CCNC|Tier2,FOXO3|Tier1,ROS1|Tier1,GOPC|Tier1,RSPO3|Tier1,PTPRK|Tier1,EPHA7|Tier2;DisruptL=;DisruptR=SLC2A12	no	chr6q14.1-q23.2
chr6	134006348	134216592	DEL	-7.44094370965338	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=SGK1|Tier2;DisruptL=SLC2A12;DisruptR=SGK1	yes	chr6q23.2
chr6	134216593	149186361	DEL	-0.339404323305801	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=MYB|Tier1,BCLAF1|Tier2,TNFAIP3|Tier1,ECT2L|Tier2;DisruptL=SGK1;DisruptR=	yes	chr6q23.2-q25.1
chr6	149186362	149655900	DUP	0.331481108739125	bicseq2	HCC1187_80--HCC-1187BL_40	known=;DisruptL=;DisruptR=	yes	chr6q25.1
chr6	149655901	170740360	DEL	-0.394475328950363	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=EZR|Tier1,FGFR1OP|Tier1,ARID1B|Tier1,QKI|Tier1,MLLT4|Tier1,ESR1|Tier1;DisruptL=;DisruptR=	no	chr6q25.1-q27
chr7	16339	149545816	DUP	0.614059996773025	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=HOXA11|Tier1,HOXA13|Tier1,CARD11|Tier1,PMS2|Tier1,RAC1|Tier1,ETV1|Tier1,HNRNPA2B1|Tier1,HOXA9|Tier1,FKBP9|Tier2,SFRP4|Tier1,ZNF479|Tier2,SBDS|Tier1,POT1|Tier1,SMO|Tier1,KIAA1549|Tier2,FAM131B|Tier2,EZH2|Tier1,JAZF1|Tier2,EGFR|Tier1,ELN|Tier2,HIP1|Tier1,GRM3|Tier2,AKAP9|Tier2,CDK6|Tier1,TRRAP|Tier1,CUX1|Tier1,MET|Tier1,CREB3L2|Tier1,TRIM24|Tier1,BRAF|Tier1,SND1|Tier1,CNTNAP2|Tier2,IKZF1|Tier1;DisruptL=AC215522.3;DisruptR=	no	chr7p22.3-q36.1
chr7	149545817	159335873	DEL	-0.411715722815841	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=MNX1|Tier2,KMT2C|Tier1;DisruptL=;DisruptR=	yes	chr7q36.1-q36.3
chr8	71162	101318335	NEU	0.188373016782473	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=TCEA1|Tier1,PLAG1|Tier1,CHCHD7|Tier1,HEY1|Tier1,COX6C|Tier2,ARHGEF10|Tier2,LEPROTL1|Tier2,WHSC1L1|Tier1,FGFR1|Tier1,IKBKB|Tier1,NBN|Tier1,CDH17|Tier2,PABPC1|Tier2,PCM1|Tier1,WRN|Tier1,NRG1|Tier1,ANK1|Tier2,NCOA2|Tier1,RUNX1T1|Tier1,HOOK3|Tier1,PREX2|Tier1,CNBD1|Tier2;DisruptL=;DisruptR=	no	chr8p23.3-q22.3
chr8	101318336	101478031	DUP	0.927379103959977	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=;DisruptR=AP001207.3	yes	chr8q22.3
chr8	101478032	123656900	DUP	0.209156037101018	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=EIF3E|Tier1,RAD21|Tier1,UBR5|Tier1,EXT1|Tier1,RSPO2|Tier1,CSMD3|Tier2;DisruptL=AP001207.3;DisruptR=AC090193.1	no	chr8q22.3-q24.13
chr8	123656901	126449871	DEL	-1.34280642685676	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=AC090193.1;DisruptR=	yes	chr8q24.13-q24.21
chr8	126449872	127768744	DUP	0.395657882128518	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=MYC|Tier1;DisruptL=;DisruptR=	yes	chr8q24.21
chr8	127768745	142901153	NEU	0.150185013836218	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=NDRG1|Tier1,FAM135B|Tier2;DisruptL=;DisruptR=GML	yes	chr8q24.21-q24.3
chr8	142901154	145078494	DUP	0.892004052186123	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=RECQL4|Tier1;DisruptL=GML;DisruptR=	yes	chr8q24.3
chr9	10000	12889208	NEU	0.186934299245523	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=CD274|Tier1,PDCD1LG2|Tier1,JAK2|Tier1,PTPRD|Tier2;DisruptL=;DisruptR=	yes	chr9p24.3-p23
chr9	12889209	13056039	DUP	1.22436154602408	bicseq2	HCC1187_80--HCC-1187BL_40	known=;DisruptL=;DisruptR=	yes	chr9p23
chr9	13056040	112114443	NEU	0.176254463288071	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=OMD|Tier2,KLF4|Tier1,TAL2|Tier1,PSIP1|Tier1,CDKN2A|Tier1,FANCG|Tier1,SYK|Tier1,PTCH1|Tier1,XPA|Tier1,NR4A3|Tier1,NFIB|Tier1,MLLT3|Tier1,PAX5|Tier1,GNAQ|Tier1,WNK2|Tier2,FANCC|Tier1;DisruptL=;DisruptR=SUSD1	no	chr9p23-q32
chr9	112114444	112332600	DUP	1.00673388643928	bicseq2	HCC1187_80--HCC-1187BL_40	known=;DisruptL=SUSD1;DisruptR=PTBP3	yes	chr9q32
chr9	112332601	138313848	NEU	0.164285592426083	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=SET|Tier1,ABL1|Tier1,RALGDS|Tier2,BRD3|Tier1,NOTCH1|Tier1,TNC|Tier2,CNTRL|Tier1,PPP6C|Tier1,NUP214|Tier1,TSC1|Tier1,FNBP1|Tier2;DisruptL=PTBP3;DisruptR=	no	chr9q32-q34.3
chr10	10287	1138217	DUP	0.883988585146988	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=LARP4B|Tier2;DisruptL=;DisruptR=	yes	chr10p15.3
chr10	1138218	1549130	NEU	0.0960742775882764	bicseq2	HCC1187_80--HCC-1187BL_40	known=DGV;COSMIC;DisruptL=;DisruptR=ADARB2-AS1,ADARB2	yes	chr10p15.3
chr10	1549131	22502952	DUP	0.901312243567163	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=KLF6|Tier1,GATA3|Tier1,MLLT10|Tier1;DisruptL=ADARB2-AS1,ADARB2;DisruptR=	no	chr10p15.3-p12.2
chr10	22502953	71740918	DUP	0.216589885939333	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=NCOA4|Tier1,ABI1|Tier1,KIF5B|Tier1,PRF1|Tier1,RET|Tier1,A1CF|Tier2,CCDC6|Tier1,TET1|Tier1,ZEB1|Tier2;DisruptL=;DisruptR=CDH23	no	chr10p12.2-q22.1
chr10	71740919	77999458	DUP	0.639369354353809	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=KAT6B|Tier1;DisruptL=CDH23;DisruptR=POLR3A	yes	chr10q22.1-q22.3
chr10	77999459	82676186	DUP	1.22176479163763	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=NUTM2B|Tier1;DisruptL=POLR3A;DisruptR=NRG3	yes	chr10q22.3-q23.1
chr10	82676187	133787316	DEL	-0.396914558297883	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=TLX1|Tier1,NUTM2A|Tier1,CYP2C8|Tier2,NFKB2|Tier1,BMPR1A|Tier1,PTEN|Tier1,FAS|Tier1,CPEB3|Tier2,SUFU|Tier1,NT5C2|Tier1,VTI1A|Tier2,TCF7L2|Tier1,KIAA1598|Tier2,FGFR2|Tier1,MGMT|Tier2;DisruptL=NRG3;DisruptR=	no	chr10q23.1-q26.3
chr11	128355	5558211	DEL	-0.642000875673019	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=HRAS|Tier1,NUP98|Tier1,CARS|Tier1;DisruptL=LINC01001;DisruptR=OR52B5P,AC104389.4	yes	chr11p15.5-p15.4
chr11	5558212	9130419	DUP	0.308843848426564	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=LMO1|Tier1;DisruptL=OR52B5P,AC104389.4;DisruptR=SCUBE2	yes	chr11p15.4
chr11	9130420	10460500	NEU	-0.0641902580462587	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=SCUBE2;DisruptR=AMPD3	yes	chr11p15.4
chr11	10460501	78421457	DUP	0.318650076781129	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=MYOD1|Tier1,FANCF|Tier1,CLP1|Tier2,FEN1|Tier2,MEN1|Tier1,MALAT1|Tier2,WT1|Tier1,LMO2|Tier1,CREB3L1|Tier1,DDB2|Tier1,SDHAF2|Tier1,CCND1|Tier1,NUMA1|Tier1,EXT2|Tier1,CTNND1|Tier2;DisruptL=AMPD3;DisruptR=AP003086.2	no	chr11p15.4-q14.1
chr11	78421458	90936582	DEL	-0.630749844247858	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=EED|Tier2,PICALM|Tier1;DisruptL=AP003086.2;DisruptR=	yes	chr11q14.1-q14.3
chr11	90936583	135076522	DUP	0.305483625064655	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=SDHD|Tier1,KCNJ5|Tier1,FAT3|Tier2,BIRC3|Tier1,POU2AF1|Tier1,PAFAH1B2|Tier1,DDX6|Tier1,BCL9L|Tier1,FOXR1|Tier2,MAML2|Tier1,ATM|Tier1,DDX10|Tier1,ZBTB16|Tier1,CBL|Tier1,ARHGEF12|Tier1,FLI1|Tier1,KMT2A|Tier1;DisruptL=;DisruptR=	no	chr11q14.3-q25
chr12	41087	28617172	DUP	0.581848560549573	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=PTPN6|Tier2,CDKN1B|Tier1,KDM5A|Tier1,CCND2|Tier1,CHD4|Tier1,ZNF384|Tier1,KRAS|Tier1,ETV6|Tier1,ETNK1|Tier1,PPFIBP1|Tier1,ERC1|Tier1;DisruptL=;DisruptR=	no	chr12p13.33-p11.22
chr12	28617173	128424712	DEL	-0.365989565983636	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=HOXC13|Tier1,HOXC11|Tier1,NAB2|Tier1,GLI1|Tier2,DDIT3|Tier1,CDK4|Tier1,BTG1|Tier1,TBX3|Tier1,SETD1B|Tier2,COL2A1|Tier1,KMT2D|Tier1,PRPF40B|Tier2,SMARCD1|Tier1,ATF1|Tier1,NACA|Tier2,STAT6|Tier1,LRIG3|Tier1,WIF1|Tier1,PTPRB|Tier1,USP44|Tier2,SH2B3|Tier1,ZCCHC8|Tier2,ARID2|Tier1,ERBB3|Tier1,HMGA2|Tier1,MDM2|Tier1,CHST11|Tier2,ALDH2|Tier2,PTPN11|Tier1,HNF1A|Tier1,BCL7A|Tier1,CLIP1|Tier1,NCOR2|Tier1;DisruptL=;DisruptR=TMEM132C	no	chr12p11.22-q24.32
chr12	128424713	129071465	DEL	-1.42555599752915	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=TMEM132C;DisruptR=	yes	chr12q24.32-q24.33
chr12	129071466	133264924	DEL	-0.43719045492461	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=POLE|Tier1;DisruptL=;DisruptR=	yes	chr12q24.33
chr13	16166247	58800127	NEU	-0.033945077283531	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=CYSLTR2|Tier2,CDX2|Tier1,ZNF198|Tier1,FLT3|Tier1,BRCA2|Tier1,LHFP|Tier2,FOXO1|Tier1,RB1|Tier1,NBEA|Tier2,LCP1|Tier2;DisruptL=;DisruptR=	no	chr13p11.2-q21.1
chr13	58800128	88970765	DEL	-1.54235715814595	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=;DisruptR=	no	chr13q21.1-q31.2
chr13	88970766	102428502	DUP	0.401403533964384	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=SOX21|Tier2,GPC5|Tier2;DisruptL=;DisruptR=	yes	chr13q31.2-q33.1
chr13	102428503	102801717	DUP	0.99987888321771	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=;DisruptR=BIVM,BIVM-ERCC5	yes	chr13q33.1
chr13	102801718	114354111	DUP	0.381722493386119	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=ERCC5|Tier1;DisruptL=BIVM,BIVM-ERCC5;DisruptR=	yes	chr13q33.1-q34
chr14	16140244	39133588	DEL	-0.566117775049862	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=NKX2-1|Tier1,FOXA1|Tier1,CCNB1IP1|Tier1,ARHGAP5|Tier2,BAZ1A|Tier2;DisruptL=;DisruptR=GEMIN2	no	chr14p11.1-q21.1
chr14	39133589	39342722	DUP	0.493451804244925	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=GEMIN2;DisruptR=MIA2	yes	chr14q21.1
chr14	39342723	41140316	DEL	-0.563269280610381	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=MIA2;DisruptR=	yes	chr14q21.1
chr14	41140317	41200380	DEL	-7.8899618415955	bicseq2	HCC1187_80--HCC-1187BL_40	known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr14q21.1
chr14	41200381	63236251	DEL	-0.553737648599806	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=SIX1|Tier1,NIN|Tier1,KTN1|Tier1,HIF1A|Tier1;DisruptL=;DisruptR=RHOJ	no	chr14q21.1-q23.2
chr14	63236252	63870830	DEL	-7.48532285813149	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=RHOJ;DisruptR=SYNE2	yes	chr14q23.2
chr14	63870831	64117654	DEL	-0.548305376763793	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=SYNE2;DisruptR=ESR2,SYNE2	yes	chr14q23.2
chr14	64117655	64374266	DUP	0.394161668186838	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=ESR2,SYNE2;DisruptR=TEX21P	yes	chr14q23.2-q23.3
chr14	64374267	68302167	DEL	-0.531674942021359	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=MAX|Tier1,RAD51B|Tier1,GPHN|Tier1;DisruptL=TEX21P;DisruptR=RAD51B	yes	chr14q23.3-q24.1
chr14	68302168	68621129	DUP	0.555575402374486	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=RAD51B|Tier1;DisruptL=RAD51B;DisruptR=RAD51B	yes	chr14q24.1
chr14	68621130	73199736	DEL	-0.549027942732434	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=RAD51B;DisruptR=PSEN1	yes	chr14q24.1-q24.2
chr14	73199737	106883618	NEU	0.00853088604767044	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=TCL1A|Tier1,DICER1|Tier1,AKT1|Tier1,TSHR|Tier1,TRIP11|Tier1,GOLGA5|Tier1,BCL11B|Tier1,HSP90AA1|Tier1;DisruptL=PSEN1;DisruptR=	no	chr14q24.2-q32.33
chr15	17083473	34410561	DEL	-0.41117399119303	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=NUTM1|Tier1;DisruptL=;DisruptR=AC025678.2,GOLGA8A	yes	chr15p11.2-q14
chr15	34410562	34526119	DEL	-7.25267317252097	bicseq2	HCC1187_80--HCC-1187BL_40	known=DGV,1000G;COSMIC;DisruptL=AC025678.2,GOLGA8A;DisruptR=GOLGA8B	yes	chr15q14
chr15	34526120	71887858	DEL	-0.344048642874428	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=BUB1B|Tier1,KNSTRN|Tier2,B2M|Tier1,CASC5|Tier1,USP8|Tier1,TCF12|Tier1,MAP2K1|Tier1,MYO5A|Tier1,SMAD3|Tier1;DisruptL=GOLGA8B;DisruptR=MYO9A	no	chr15q14-q23
chr15	71887859	72152243	DEL	-7.64725860747131	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=MYO9A;DisruptR=AC020779.2	yes	chr15q23
chr15	72152244	84936396	DEL	-0.369016069223351	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=PML|Tier1;DisruptL=AC020779.2;DisruptR=SLC28A1	yes	chr15q23-q25.3
chr15	84936397	85513789	DUP	0.265157248505685	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=SLC28A1;DisruptR=AKAP13	yes	chr15q25.3
chr15	85513790	90138915	DEL	-0.399800521969502	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=POLG|Tier2,IDH2|Tier1,NTRK3|Tier1;DisruptL=AKAP13;DisruptR=	yes	chr15q25.3-q26.1
chr15	90138916	90290294	DUP	0.919740716100665	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=;DisruptR=AC091167.6	yes	chr15q26.1
chr15	90290295	101981087	DEL	-0.384199249033154	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=FES|Tier1,BLM|Tier1,CRTC3|Tier1,CHD2|Tier2;DisruptL=AC091167.6;DisruptR=	yes	chr15q26.1-q26.3
chr16	10005	12896986	DEL	-0.385239180917117	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=TRAF7|Tier1,SOCS1|Tier1,RMI2|Tier1,TNFRSF17|Tier1,AXIN1|Tier1,TSC2|Tier1,RUNDC2A|Tier2,CREBBP|Tier1,GRIN2A|Tier1,CIITA|Tier1,NTHL1|Tier2;DisruptL=;DisruptR=	yes	chr16p13.3-p13.12
chr16	12896987	30065416	NEU	0.189115308851158	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=ERCC4|Tier1,PALB2|Tier1,IL21R|Tier1,MYH11|Tier1,PRKCB|Tier2;DisruptL=;DisruptR=AC093512.2,ALDOA	yes	chr16p13.12-p11.2
chr16	30065417	90226217	DEL	-0.373327567059381	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=FUS|Tier1,MAF|Tier1,CYLD|Tier1,HERPUD1|Tier1,CDH11|Tier1,CBFB|Tier1,RFWD3|Tier2,CBFA2T3|Tier1,CTCF|Tier1,CDH1|Tier1,ZFHX3|Tier1,FANCA|Tier1;DisruptL=AC093512.2,ALDOA;DisruptR=	no	chr16p11.2-q24.3
chr17	168977	39261864	DEL	-0.374808059467846	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=TP53|Tier1,YWHAE|Tier1,USP6|Tier1,PER1|Tier1,FLCN|Tier1,TAF15|Tier1,MLLT6|Tier1,LASP1|Tier1,RABEP1|Tier1,GAS7|Tier1,MAP2K4|Tier1,NCOR1|Tier1,SPECC1|Tier2,NF1|Tier1,SUZ12|Tier1;DisruptL=DOC2B;DisruptR=FBXL20	no	chr17p13.3-q12
chr17	39261865	39350014	DEL	-6.96200071348413	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=FBXL20;DisruptR=FBXL20	yes	chr17q12
chr17	39350015	83247341	DEL	-0.354179601608721	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=CCR7|Tier2,H3F3B|Tier1,SRSF2|Tier1,CANT1|Tier1,CDK12|Tier1,RARA|Tier1,ETV4|Tier1,SPOP|Tier1,RNF43|Tier1,PPM1D|Tier1,CD79B|Tier1,DDX5|Tier1,PRKAR1A|Tier1,ASPSCR1|Tier1,ERBB2|Tier1,SMARCE1|Tier1,STAT5B|Tier1,STAT3|Tier1,BRCA1|Tier1,KAT7|Tier2,COL1A1|Tier1,HLF|Tier1,MSI2|Tier1,CLTC|Tier1,BRIP1|Tier1,AXIN2|Tier1,SEPT9|Tier2,RNF213|Tier1;DisruptL=FBXL20;DisruptR=	no	chr17q12-q25.3
chr18	10010	8940325	DUP	0.616432472370027	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr18p11.32-p11.22
chr18	8940326	10814015	DUP	0.946910334509928	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=;DisruptR=PIEZO2	yes	chr18p11.22
chr18	10814016	55692428	DUP	0.603611667356124	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=SMAD2|Tier1,SMAD4|Tier1,SS18|Tier1,SETBP1|Tier1,DCC|Tier2,ZNF521|Tier1;DisruptL=PIEZO2;DisruptR=	no	chr18p11.22-q21.2
chr18	55692429	80263172	DEL	-0.406418540164903	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=KDSR|Tier1,BCL2|Tier1,MALT1|Tier1;DisruptL=;DisruptR=	no	chr18q21.2-q23
chr19	90733	5824138	DEL	-0.384511646917663	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=FSTL3|Tier1,STK11|Tier1,TCF3|Tier1,GNA11|Tier1,MAP2K2|Tier1,SH3GL1|Tier1;DisruptL=;DisruptR=NRTN	yes	chr19p13.3
chr19	5824139	37270966	DUP	0.588421332380319	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=CD209|Tier2,KEAP1|Tier1,LYL1|Tier1,CEBPA|Tier1,MLLT1|Tier1,MUC16|Tier2,CALR|Tier1,PRKACA|Tier1,DNAJB1|Tier1,BRD4|Tier1,TPM4|Tier1,JAK3|Tier1,ZNF429|Tier2,CCNE1|Tier1,VAV1|Tier2,DNM2|Tier1,SMARCA4|Tier1,ELL|Tier1,CRTC1|Tier1,CEP89|Tier2,LSM14A|Tier2;DisruptL=NRTN;DisruptR=AC016590.1	no	chr19p13.3-q13.12
chr19	37270967	50944418	NEU	0.138429182970222	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=BCL3|Tier1,BCL2L12|Tier2,KLK2|Tier1,CD79A|Tier1,CIC|Tier1,CBLC|Tier1,ERCC2|Tier1,BAX|Tier1,POLD1|Tier1,AKT2|Tier1;DisruptL=AC016590.1;DisruptR=KLK5	yes	chr19q13.12-q13.41
chr19	50944419	58607515	DUP	0.546060610911417	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=TFPT|Tier2,PPP2R1A|Tier1,ZNF331|Tier1,CNOT3|Tier1;DisruptL=KLK5;DisruptR=	yes	chr19q13.41-q13.43
chr20	67260	4273275	DUP	0.595981800732335	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=SIRPA|Tier2;DisruptL=;DisruptR=	yes	chr20p13
chr20	4273276	6218412	DUP	0.940565068186019	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr20p13-p12.3
chr20	6218413	32713333	DUP	0.610464950197394	bicseq2	HCC1187_80--HCC-1187BL_40	known=;Cancer_census=CRNKL1|Tier2,ASXL1|Tier1;DisruptL=;DisruptR=COMMD7,FO393400.1	no	chr20p12.3-q11.21
chr20	32713334	64334067	DEL	-0.389263654109862	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=MAFB|Tier1,SRC|Tier1,TOP1|Tier1,SDC4|Tier1,SALL4|Tier1,GNAS|Tier1,SS18L1|Tier1,PTK6|Tier1,PLCG1|Tier1,NFATC2|Tier1,PTPRT|Tier1;DisruptL=COMMD7,FO393400.1;DisruptR=	no	chr20q11.21-q13.33
chr21	13044018	46699872	NEU	0.197904378301741	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=OLIG2|Tier1,TMPRSS2|Tier1,U2AF1|Tier1,RUNX1|Tier1,ERG|Tier1;DisruptL=ANKRD30BP2;DisruptR=	no	chr21q11.2-q22.3
chr22	10514978	50808368	DEL	-0.391307309980917	bicseq2	HCC1187_80--HCC-1187BL_40	known=;COSMIC;Cancer_census=SEPT5|Tier2,APOBEC3B|Tier1,DGCR8|Tier2,LZTR1|Tier1,MAPK1|Tier1,SMARCB1|Tier1,ZNRF3|Tier2,EWSR1|Tier1,ZNF278|Tier1,ISX|Tier2,PDGFB|Tier1,MKL1|Tier1,CLTCL1|Tier1,BCR|Tier1,MN1|Tier1,CHEK2|Tier1,NF2|Tier1,MYH9|Tier1,EP300|Tier1;DisruptL=;DisruptR=	no	chr22p11.2-q13.33