#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	44887174	DEL	-1.72835862515757	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=P2RY8|Tier1,CRLF2|Tier1,ZRSR2|Tier1,EIF1AX|Tier2,FAM47C|Tier2,BCOR|Tier1,DDX3X|Tier1,KDM6A|Tier1;DisruptL=;DisruptR=KDM6A	no	chrXp22.33-p11.3
chrX	44887175	47658808	DEL	-0.694565389985377	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ARAF|Tier2,KDM6A|Tier1,RBM10|Tier1;DisruptL=KDM6A;DisruptR=UXT	yes	chrXp11.3-p11.23
chrX	47658809	56991083	DEL	-1.73362823584366	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SSX1|Tier1,WAS|Tier1,SSX4|Tier1,GATA1|Tier1,TFE3|Tier1,SSX2|Tier1,SMC1A|Tier2,KDM5C|Tier1;DisruptL=UXT;DisruptR=SPIN3	yes	chrXp11.23-p11.21
chrX	56991084	57362136	DEL	-1.19124972384329	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=SPIN3;DisruptR=FAAH2	yes	chrXp11.21
chrX	57362137	62463002	DEL	-0.290094828113607	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=FAAH2;DisruptR=	yes	chrXp11.21-q11.1
chrX	62463003	65750659	NEU	0.196942925594602	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=AMER1|Tier1,MSN|Tier1;DisruptL=;DisruptR=	yes	chrXq11.1-q12
chrX	65750660	73870954	NEU	-0.18078315912977	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FOXO4|Tier1,ZMYM3|Tier2,NONO|Tier1,MED12|Tier1,AR|Tier1;DisruptL=;DisruptR=	yes	chrXq12-q13.2
chrX	73870955	76241261	DUP	0.284191052933893	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chrXq13.2-q13.3
chrX	76241262	84382245	DUP	0.597238890868542	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ATRX|Tier1;DisruptL=;DisruptR=HDX	yes	chrXq13.3-q21.1
chrX	84382246	87103046	DUP	0.281663091550775	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=HDX;DisruptR=	yes	chrXq21.1-q21.31
chrX	87103047	88322772	DUP	0.585907300792039	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chrXq21.31
chrX	88322773	100877555	DUP	0.274961080990258	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chrXq21.31-q22.1
chrX	100877556	115889293	DEL	-0.630376714032877	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=IRS4|Tier1,BTK|Tier1;DisruptL=;DisruptR=	yes	chrXq22.1-q23
chrX	115889294	117971510	DUP	0.20296501661757	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=KLHL13	yes	chrXq23-q24
chrX	117971511	118882103	DUP	1.06761629630407	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=KLHL13;DisruptR=LINC01285	yes	chrXq24
chrX	118882104	139747068	DUP	0.241773480604703	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=DCAF12L2|Tier2,STAG2|Tier1,ELF4|Tier1,PHF6|Tier1,SEPT6|Tier2,GPC3|Tier1,BCORL1|Tier1;DisruptL=LINC01285;DisruptR=ATP11C	no	chrXq24-q27.1
chrX	139747069	140075558	DEL	-1.84044910106853	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ATP11C;DisruptR=	yes	chrXq27.1
chrX	140075559	153146260	DEL	-0.799890428740223	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chrXq27.1-q28
chrX	153149106	153586440	DUP	0.433126799532363	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=ATP2B3|Tier1;DisruptL=;DisruptR=	yes	chrXq28
chrX	153586441	156030795	NEU	-0.187843086585314	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=RPL10|Tier1,MTCP1|Tier1,FLNA|Tier2;DisruptL=;DisruptR=	yes	chrXq28
chr1	10028	6465256	NEU	0.156075871411797	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=TNFRSF14|Tier1,SKI|Tier2,RPL22|Tier1,PRDM16|Tier1;DisruptL=;DisruptR=TNFRSF25	yes	chr1p36.33-p36.31
chr1	6465257	8673895	NEU	-0.121931046820047	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CAMTA1|Tier1;DisruptL=TNFRSF25;DisruptR=RERE	yes	chr1p36.31-p36.23
chr1	8673896	8950766	DUP	0.656023234252009	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=RERE;DisruptR=CA6	yes	chr1p36.23
chr1	8950767	19771880	NEU	-0.186864824999868	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CASP9|Tier2,PAX7|Tier1,MTOR|Tier1,PRDM2|Tier2,SPEN|Tier1,SDHB|Tier1,ARHGEF10L|Tier2;DisruptL=CA6;DisruptR=TMCO4	yes	chr1p36.23-p36.13
chr1	19771881	23062690	DUP	0.237450851430329	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=TMCO4;DisruptR=KDM1A,AL031428.1	yes	chr1p36.13-p36.12
chr1	23062691	47818751	NEU	-0.159590139641788	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ID3|Tier2,MDS2|Tier2,MYCL|Tier1,TAL1|Tier1,LCK|Tier1,SFPQ|Tier1,THRAP3|Tier2,CSF3R|Tier1,MPL|Tier1,MUTYH|Tier1,STIL|Tier1,ARID1A|Tier1;DisruptL=KDM1A,AL031428.1;DisruptR=AC096541.1,TRABD2B	no	chr1p36.12-p33
chr1	47818752	51383048	DUP	0.227408194078326	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CDKN2C|Tier1,EPS15|Tier1;DisruptL=AC096541.1,TRABD2B;DisruptR=EPS15	yes	chr1p33-p32.3
chr1	51383049	83866322	NEU	-0.15707767060226	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=JUN|Tier1,FUBP1|Tier1,JAK1|Tier1,EPS15|Tier1;DisruptL=EPS15;DisruptR=TTLL7	no	chr1p32.3-p31.1
chr1	83866323	84290001	DUP	0.644914417751449	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=TTLL7;DisruptR=	yes	chr1p31.1
chr1	84290002	94125487	NEU	-0.137787151804375	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=BCL10|Tier1,RPL5|Tier1;DisruptL=;DisruptR=	yes	chr1p31.1-p22.1
chr1	94125488	94476955	DUP	0.668619353510406	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=ABCD3	yes	chr1p22.1-p21.3
chr1	94476956	103478704	NEU	-0.144879163976794	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ABCD3;DisruptR=AC095032.1	yes	chr1p21.3-p21.1
chr1	103478705	107356812	DEL	-0.744646889607662	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AC095032.1;DisruptR=NTNG1	yes	chr1p21.1-p13.3
chr1	107356813	150474751	NEU	-0.151046496273773	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=RBM15|Tier1,NRAS|Tier1,FAM46C|Tier1,BCL9|Tier1,TRIM33|Tier1,NOTCH2|Tier1,ATP1A1|Tier1,PDE4DIP|Tier1;DisruptL=NTNG1;DisruptR=RPRD2	no	chr1p13.3-q21.2
chr1	150474752	150749711	DUP	0.683474237545922	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV;COSMIC;DisruptL=RPRD2;DisruptR=CTSS	yes	chr1q21.2-q21.3
chr1	150749712	186671316	NEU	-0.113137191201457	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MLLT11|Tier1,S100A7|Tier2,TPM3|Tier1,LMNA|Tier1,PRCC|Tier1,NTRK1|Tier1,FCRL4|Tier1,FCGR2B|Tier1,DDR2|Tier1,PRRX1|Tier1,ABL2|Tier1,TPR|Tier1,ARNT|Tier1,SDHC|Tier1,MUC1|Tier1,PBX1|Tier1;DisruptL=CTSS;DisruptR=	no	chr1q21.3-q31.1
chr1	186671317	203360618	DUP	0.282790700232082	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ELF3|Tier2,CDC73|Tier1,PTPRC|Tier1;DisruptL=;DisruptR=	yes	chr1q31.1-q32.1
chr1	203360619	205097986	DUP	0.735659195686188	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MDM4|Tier1;DisruptL=;DisruptR=RBBP5	yes	chr1q32.1
chr1	205097987	212301636	DUP	0.460614398395344	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SLC45A3|Tier1,ELK4|Tier1;DisruptL=RBBP5;DisruptR=AL360091.3,PPP2R5A	yes	chr1q32.1-q32.3
chr1	212301637	212996331	DUP	0.955781894938254	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AL360091.3,PPP2R5A;DisruptR=ANGEL2	yes	chr1q32.3
chr1	212996332	217777417	DUP	0.578477211507027	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ANGEL2;DisruptR=SPATA17	yes	chr1q32.3-q41
chr1	217777418	220805515	DUP	0.888503013652749	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=SPATA17;DisruptR=MARC1	yes	chr1q41
chr1	220805516	223431562	DUP	1.12970587737484	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=MARC1;DisruptR=	yes	chr1q41
chr1	223431563	234776417	NEU	-0.122934466399223	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=H3F3A|Tier1;DisruptL=;DisruptR=	yes	chr1q41-q42.3
chr1	234776418	242120886	DUP	0.28530012169613	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FH|Tier1,RGS7|Tier2;DisruptL=;DisruptR=PLD5	yes	chr1q42.3-q43
chr1	242120887	248946322	DUP	0.568056979693817	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=AKT3|Tier2;DisruptL=PLD5;DisruptR=	yes	chr1q43-q44
chr2	10005	37783334	DEL	-0.666161183621444	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MYCN|Tier1,C2orf44|Tier1,NCOA1|Tier1,ASXL2|Tier2,DNMT3A|Tier1,STRN|Tier1,ALK|Tier1,BIRC6|Tier2;DisruptL=;DisruptR=	no	chr2p25.3-p22.2
chr2	37783335	62620651	DEL	-0.246526088017794	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SIX2|Tier2,EPAS1|Tier1,MSH6|Tier1,FBXO11|Tier1,BCL11A|Tier1,REL|Tier1,XPO1|Tier1,EML4|Tier1,MSH2|Tier1;DisruptL=;DisruptR=AC092155.1	no	chr2p22.2-p15
chr2	63608437	94141931	DEL	-0.638579739077769	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=PCBP1|Tier2,DCTN1|Tier1;DisruptL=WDPCP;DisruptR=	no	chr2p15-q11.1
chr2	95642457	105668984	DEL	-0.302118666495722	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=TMEM127|Tier1,AFF3|Tier1;DisruptL=;DisruptR=	yes	chr2q11.1-q12.2
chr2	105668985	109199259	DEL	-0.697224317536778	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=RANBP2|Tier1,RGPD3|Tier2;DisruptL=;DisruptR=SH3RF3	yes	chr2q12.2-q13
chr2	109199785	114973555	DEL	-0.401017947371023	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=PAX8|Tier1;DisruptL=SH3RF3;DisruptR=DPP10	yes	chr2q13-q14.1
chr2	114973556	242183395	DEL	-0.708750166909801	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CXCR4|Tier1,HOXD13|Tier1,HOXD11|Tier1,FEV|Tier1,ACKR3|Tier1,ACVR1|Tier1,NFE2L2|Tier1,CASP8|Tier1,CD28|Tier2,CREB1|Tier1,IDH1|Tier1,BARD1|Tier1,ATIC|Tier1,ACSL3|Tier1,ERCC3|Tier1,COL3A1|Tier2,SF3B1|Tier1,CUL3|Tier2,LRP1B|Tier1,ACVR2A|Tier1,ITGAV|Tier2,PMS1|Tier2,ERBB4|Tier1,PAX3|Tier1;DisruptL=DPP10;DisruptR=	no	chr2q14.1-q37.3
chr3	10005	9676503	NEU	-0.167671281007473	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SRGAP3|Tier2;DisruptL=;DisruptR=MTMR14	yes	chr3p26.3-p25.3
chr3	9676504	10083193	DUP	0.814738918686967	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FANCD2|Tier1;DisruptL=MTMR14;DisruptR=FANCD2,FANCD2OS	yes	chr3p25.3
chr3	10083194	39770242	NEU	-0.150570446358918	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=VHL|Tier1,CCR4|Tier2,MYD88|Tier1,PPARG|Tier1,RAF1|Tier1,MLH1|Tier1,FANCD2|Tier1,XPC|Tier1,TGFBR2|Tier1,FBLN2|Tier2;DisruptL=FANCD2,FANCD2OS;DisruptR=	no	chr3p25.3-p22.1
chr3	39770243	41312675	DUP	0.782925396820896	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CTNNB1|Tier1;DisruptL=;DisruptR=ULK4	yes	chr3p22.1
chr3	41312676	52565237	DEL	-0.741873286549981	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=BAP1|Tier1,NCKIPSD|Tier2,RHOA|Tier1,SETD2|Tier1,PBRM1|Tier1;DisruptL=ULK4;DisruptR=SMIM4,PBRM1	yes	chr3p22.1-p21.1
chr3	52565238	52629453	DEL	-6.70583121458386	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=PBRM1|Tier1;DisruptL=SMIM4,PBRM1;DisruptR=PBRM1	yes	chr3p21.1
chr3	52629454	85183522	DEL	-0.75790028087575	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MITF|Tier1,PBRM1|Tier1,CACNA1D|Tier1,FOXP1|Tier1,FHIT|Tier1,ROBO2|Tier2;DisruptL=PBRM1;DisruptR=CADM2	no	chr3p21.1-p12.1
chr3	85183523	93455911	DUP	0.299003383510322	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=EPHA3|Tier2;DisruptL=CADM2;DisruptR=	yes	chr3p12.1-q11.1
chr3	93481450	95006070	DUP	0.700039126851439	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=LINC00879	yes	chr3q11.1-q11.2
chr3	95006071	170316551	DUP	0.28140904259424	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FOXL2|Tier1,TFG|Tier1,GATA2|Tier1,RPN1|Tier1,CNBP|Tier1,GMPS|Tier2,MECOM|Tier1,CBLB|Tier1,POLQ|Tier1,STAG1|Tier2,PIK3CB|Tier1,ATR|Tier1,WWTR1|Tier1,MLF1|Tier1;DisruptL=LINC00879;DisruptR=	no	chr3q11.2-q26.2
chr3	170316552	173658862	DUP	0.678692770376269	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=NLGN1	yes	chr3q26.2-q26.31
chr3	173658863	194247703	DUP	0.34167496868608	bicseq2	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	no	chr3q26.31-q29
chr3	194247704	198139690	DUP	0.6452692727476	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MUC4|Tier2,TFRC|Tier2;DisruptL=LINC02036,LINC02037;DisruptR=	yes	chr3q29
chr4	10011	14827697	DEL	-0.323205446325438	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FGFR3|Tier1,WHSC1|Tier1;DisruptL=;DisruptR=LINC00504	yes	chr4p16.3-p15.33
chr4	14827698	15665043	DUP	0.485069016820572	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=LINC00504;DisruptR=FBXL5	yes	chr4p15.33-p15.32
chr4	15665044	52771463	DEL	-0.25234639669229	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=RHOH|Tier1,SLC34A2|Tier1,PHOX2B|Tier1,TEC|Tier2,N4BP2|Tier2;DisruptL=FBXL5;DisruptR=	no	chr4p15.32-q12
chr4	52771464	57019041	DUP	0.629558682844074	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FIP1L1|Tier1,CHIC2|Tier2,KIT|Tier1,KDR|Tier1,PDGFRA|Tier1;DisruptL=;DisruptR=POLR2B	yes	chr4q12
chr4	57019042	59832663	DUP	0.87211026187151	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=POLR2B;DisruptR=	yes	chr4q12-q13.1
chr4	59832664	62845465	DEL	-0.740857175621992	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr4q13.1
chr4	62845466	65266704	DUP	1.03716491555247	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV;COSMIC;DisruptL=;DisruptR=	yes	chr4q13.1
chr4	65266705	91384037	DEL	-0.707239514593161	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=PTPN13|Tier1,AFF1|Tier1;DisruptL=;DisruptR=CCSER1	no	chr4q13.1-q22.1
chr4	91384038	91964419	DEL	-7.54755497064979	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV;COSMIC;DisruptL=CCSER1;DisruptR=	yes	chr4q22.1
chr4	91964420	190066290	DEL	-0.716037142658379	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=IL2|Tier1,FBXW7|Tier1,CASP3|Tier2,RAP1GDS1|Tier1,TET2|Tier1,LEF1|Tier1,FAT4|Tier1,FAT1|Tier1;DisruptL=;DisruptR=DBET	no	chr4q22.1-q35.2
chr5	11484	12810903	DUP	0.774789132660277	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SDHA|Tier1,TERT|Tier1,CTNND2|Tier2;DisruptL=;DisruptR=	yes	chr5p15.33-p15.2
chr5	12810904	32366972	DUP	0.651512150845754	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CDH10|Tier2,DROSHA|Tier1;DisruptL=;DisruptR=ZFR	yes	chr5p15.2-p13.3
chr5	32366973	164930824	DUP	0.26150278738221	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=RAD17|Tier2,IL7R|Tier1,LIFR|Tier1,MAP3K1|Tier1,APC|Tier1,PDGFRB|Tier1,CD74|Tier1,ITK|Tier1,PWWP2A|Tier2,IL6ST|Tier1,PIK3R1|Tier1,ACSL6|Tier2,AFF4|Tier1,ARHGAP26|Tier1,CSF1R|Tier2,EBF1|Tier1;DisruptL=ZFR;DisruptR=AC109466.1	no	chr5p13.3-q34
chr5	164930825	180949083	DUP	0.652483122965833	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=NPM1|Tier1,FGFR4|Tier1,TLX3|Tier1,FLT4|Tier1,NSD1|Tier1;DisruptL=AC109466.1;DisruptR=BTNL8	yes	chr5q34-q35.3
chr5	180949084	181003477	DEL	-7.28478800467449	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV,1000G;COSMIC;DisruptL=BTNL8;DisruptR=BTNL3	yes	chr5q35.3
chr5	181003478	181449255	DUP	0.607174042125907	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=BTNL3;DisruptR=	yes	chr5q35.3
chr6	89830	607294	NEU	-0.0974955267155547	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV;COSMIC;Cancer_census=IRF4|Tier1;DisruptL=;DisruptR=EXOC2	yes	chr6p25.3
chr6	607295	882087	DEL	-1.67205910329414	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV;DisruptL=EXOC2;DisruptR=	yes	chr6p25.3
chr6	882088	24909815	NEU	-0.0481369085644811	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=DEK|Tier1;DisruptL=;DisruptR=RIPOR2	no	chr6p25.3-p22.3
chr6	24909816	32487100	DEL	-0.655441971510541	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=HIST1H3B|Tier1,HIST1H4I|Tier1,HLA-A|Tier1,POU5F1|Tier1,TRIM27|Tier1;DisruptL=RIPOR2;DisruptR=	yes	chr6p22.3-p21.32
chr6	32487101	36092705	DUP	0.299104647061063	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=DAXX|Tier1,HMGA1|Tier1,FANCE|Tier1;DisruptL=;DisruptR=MAPK14	yes	chr6p21.32-p21.31
chr6	36092706	37946968	NEU	-0.0998902943169236	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CDKN1A|Tier2,PIM1|Tier1,SRSF3|Tier1;DisruptL=MAPK14;DisruptR=ZFAND3	yes	chr6p21.31-p21.2
chr6	37946969	38141254	DUP	1.18179918193363	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ZFAND3;DisruptR=ZFAND3	yes	chr6p21.2
chr6	38141255	41251984	DUP	0.546902991511211	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ZFAND3;DisruptR=	yes	chr6p21.2-p21.1
chr6	41251985	52220478	DUP	0.29381412204373	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=TFEB|Tier1,CCND3|Tier1,NFKBIE|Tier1,HSP90AB1|Tier1;DisruptL=;DisruptR=	yes	chr6p21.1-p12.2
chr6	52220479	52679253	DUP	0.676611067236661	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=TMEM14A	yes	chr6p12.2
chr6	52679254	54303455	NEU	-0.112876231335924	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=TMEM14A;DisruptR=	yes	chr6p12.2-p12.1
chr6	54303456	54849666	DEL	-0.667579826586544	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=FAM83B	yes	chr6p12.1
chr6	54849667	59823890	DEL	-1.59872872831292	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=BMP5|Tier2;DisruptL=FAM83B;DisruptR=	yes	chr6p12.1-q11.1
chr6	60241646	78257462	NEU	0.160918441759702	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr6q11.1-q14.1
chr6	78257463	78326601	DEL	-6.72298213570793	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr6q14.1
chr6	78326602	129707604	NEU	0.151128061967344	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=PRDM1|Tier1,CCNC|Tier2,FOXO3|Tier1,ROS1|Tier1,GOPC|Tier1,RSPO3|Tier1,PTPRK|Tier1,EPHA7|Tier2;DisruptL=;DisruptR=ARHGAP18	no	chr6q14.1-q22.33
chr6	129707605	130004066	DUP	1.13597980109605	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ARHGAP18;DisruptR=	yes	chr6q22.33-q23.1
chr6	130004067	166890852	NEU	0.135162825773773	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SGK1|Tier2,MYB|Tier1,BCLAF1|Tier2,TNFAIP3|Tier1,ECT2L|Tier2,EZR|Tier1,ARID1B|Tier1,QKI|Tier1,ESR1|Tier1;DisruptL=;DisruptR=AL159163.1,RPS6KA2	no	chr6q23.1-q27
chr6	166890853	170740360	DUP	0.384229191124336	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FGFR1OP|Tier1,MLLT4|Tier1;DisruptL=AL159163.1,RPS6KA2;DisruptR=	yes	chr6q27
chr7	16339	43477638	DEL	-0.560472225550679	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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,JAZF1|Tier2;DisruptL=AC215522.3;DisruptR=HECW1	no	chr7p22.3-p13
chr7	43477639	57487363	DUP	0.628437964902542	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ZNF479|Tier2,EGFR|Tier1,IKZF1|Tier1;DisruptL=HECW1;DisruptR=	yes	chr7p13-p11.2
chr7	57497083	62116180	DUP	0.956606549618036	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=	yes	chr7p11.2-q11.21
chr7	62454737	62742671	DEL	-0.241455263265728	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr7q11.21
chr7	62742672	69920123	DEL	-0.794219457563331	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SBDS|Tier1;DisruptL=;DisruptR=AUTS2	yes	chr7q11.21-q11.22
chr7	69920124	70236679	DEL	-1.79218990733236	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AUTS2;DisruptR=AUTS2	yes	chr7q11.22
chr7	70236680	84167574	DEL	-0.735132612830231	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ELN|Tier2,HIP1|Tier1;DisruptL=AUTS2;DisruptR=SEMA3A	yes	chr7q11.22-q21.11
chr7	84167575	84789192	NEU	-0.0513236645344638	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=SEMA3A;DisruptR=	yes	chr7q21.11
chr7	84789193	116918672	DEL	-0.728996603528486	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=GRM3|Tier2,AKAP9|Tier2,CDK6|Tier1,TRRAP|Tier1,CUX1|Tier1,MET|Tier1;DisruptL=;DisruptR=CAPZA2	no	chr7q21.11-q31.2
chr7	116918673	125702340	NEU	-0.162684801865387	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=POT1|Tier1;DisruptL=CAPZA2;DisruptR=	yes	chr7q31.2-q31.33
chr7	125702341	137445253	DEL	-0.745998252095981	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SMO|Tier1,SND1|Tier1;DisruptL=;DisruptR=DGKI	yes	chr7q31.33-q33
chr7	137445254	144556895	NEU	-0.156912493019675	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=KIAA1549|Tier2,FAM131B|Tier2,CREB3L2|Tier1,TRIM24|Tier1,BRAF|Tier1;DisruptL=DGKI;DisruptR=TPK1	yes	chr7q33-q35
chr7	144556896	159335873	DEL	-0.778625101618424	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=EZH2|Tier1,MNX1|Tier2,KMT2C|Tier1,CNTNAP2|Tier2;DisruptL=TPK1;DisruptR=	yes	chr7q35-q36.3
chr8	71162	36461420	DEL	-0.744171849575792	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ARHGEF10|Tier2,LEPROTL1|Tier2,PCM1|Tier1,WRN|Tier1,NRG1|Tier1;DisruptL=;DisruptR=	no	chr8p23.3-p12
chr8	36461421	43475932	NEU	-0.154733083073201	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=WHSC1L1|Tier1,FGFR1|Tier1,IKBKB|Tier1,ANK1|Tier2,HOOK3|Tier1;DisruptL=;DisruptR=	yes	chr8p12-p11.1
chr8	43475933	43646293	DUP	1.92099540682375	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=	yes	chr8p11.1
chr8	43646294	45740170	NEU	-0.12482842486346	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=	yes	chr8p11.1-q11.1
chr8	45740171	60480053	DUP	0.718053896512785	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=TCEA1|Tier1,PLAG1|Tier1,CHCHD7|Tier1;DisruptL=;DisruptR=LINC01301	yes	chr8q11.1-q12.1
chr8	60480054	69321950	DUP	0.941090217671376	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=PREX2|Tier1;DisruptL=LINC01301;DisruptR=	yes	chr8q12.1-q13.2
chr8	69321951	96324265	DUP	0.69922561572035	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=HEY1|Tier1,NBN|Tier1,CDH17|Tier2,NCOA2|Tier1,RUNX1T1|Tier1,CNBD1|Tier2;DisruptL=;DisruptR=PTDSS1	no	chr8q13.2-q22.1
chr8	96324266	97238481	DUP	1.06765311578853	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=PTDSS1;DisruptR=	yes	chr8q22.1
chr8	97238482	101450436	DUP	0.712334816273699	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=COX6C|Tier2,PABPC1|Tier2;DisruptL=;DisruptR=AP001208.2	yes	chr8q22.1-q22.3
chr8	101450437	113801448	DUP	1.46774209690245	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=EIF3E|Tier1,UBR5|Tier1,RSPO2|Tier1,CSMD3|Tier2;DisruptL=AP001208.2;DisruptR=	yes	chr8q22.3-q23.3
chr8	113801449	114412377	DUP	0.717790645332516	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=	yes	chr8q23.3
chr8	114412378	121698090	DUP	1.13189741236656	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=RAD21|Tier1,EXT1|Tier1;DisruptL=;DisruptR=AC104233.1	yes	chr8q23.3-q24.13
chr8	121698091	145078494	DUP	1.22452168263268	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MYC|Tier1,RECQL4|Tier1,NDRG1|Tier1,FAM135B|Tier2;DisruptL=AC104233.1;DisruptR=	no	chr8q24.13-q24.3
chr9	10000	28551864	DEL	-1.48257630766413	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CD274|Tier1,PDCD1LG2|Tier1,PSIP1|Tier1,CDKN2A|Tier1,JAK2|Tier1,NFIB|Tier1,MLLT3|Tier1,PTPRD|Tier2;DisruptL=;DisruptR=LINGO2	no	chr9p24.3-p21.1
chr9	28551865	30540068	DUP	0.706699117415695	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=LINGO2;DisruptR=LINC01242	yes	chr9p21.1
chr9	30540069	45516998	NEU	-0.053178330592203	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=FANCG|Tier1,PAX5|Tier1;DisruptL=LINC01242;DisruptR=	yes	chr9p21.1-q12
chr9	45516999	65515654	DEL	-0.795656898705764	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=	yes	chr9q12-q21.11
chr9	65515655	138313848	NEU	-0.154395568154376	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=OMD|Tier2,KLF4|Tier1,TAL2|Tier1,SET|Tier1,SYK|Tier1,PTCH1|Tier1,XPA|Tier1,NR4A3|Tier1,ABL1|Tier1,RALGDS|Tier2,BRD3|Tier1,NOTCH1|Tier1,GNAQ|Tier1,WNK2|Tier2,FANCC|Tier1,TNC|Tier2,CNTRL|Tier1,PPP6C|Tier1,NUP214|Tier1,TSC1|Tier1,FNBP1|Tier2;DisruptL=;DisruptR=	no	chr9q21.11-q34.3
chr10	10287	3335245	DUP	0.361671598654202	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=LARP4B|Tier2;DisruptL=;DisruptR=	yes	chr10p15.3-p15.2
chr10	3335246	23965103	DUP	0.66547076243248	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=KLF6|Tier1,GATA3|Tier1,MLLT10|Tier1;DisruptL=;DisruptR=KIAA1217	no	chr10p15.2-p12.2
chr10	23965104	27756913	DUP	0.966580709081905	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ABI1|Tier1;DisruptL=KIAA1217;DisruptR=MKX-AS1	yes	chr10p12.2-p12.1
chr10	27756914	29240215	DUP	0.691298585249938	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=MKX-AS1;DisruptR=	yes	chr10p12.1
chr10	29240216	37167257	DUP	0.246423972790427	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=KIF5B|Tier1,ZEB1|Tier2;DisruptL=;DisruptR=ANKRD30A	yes	chr10p12.1-p11.21
chr10	37167258	39580116	DUP	0.532737884403954	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=ANKRD30A;DisruptR=	yes	chr10p11.21-p11.1
chr10	39580117	63904555	DUP	0.353803273347237	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=NCOA4|Tier1,RET|Tier1,A1CF|Tier2,CCDC6|Tier1;DisruptL=;DisruptR=AC022387.1	no	chr10p11.1-q21.3
chr10	63904556	133787316	NEU	-0.178572977140871	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=TLX1|Tier1,PRF1|Tier1,NUTM2B|Tier1,NUTM2A|Tier1,CYP2C8|Tier2,NFKB2|Tier1,TET1|Tier1,KAT6B|Tier1,BMPR1A|Tier1,PTEN|Tier1,FAS|Tier1,CPEB3|Tier2,SUFU|Tier1,NT5C2|Tier1,VTI1A|Tier2,TCF7L2|Tier1,KIAA1598|Tier2,FGFR2|Tier1,MGMT|Tier2;DisruptL=AC022387.1;DisruptR=	no	chr10q21.3-q26.3
chr11	128355	4827727	NEU	-0.232843103710957	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=HRAS|Tier1,NUP98|Tier1,CARS|Tier1;DisruptL=LINC01001;DisruptR=MMP26	yes	chr11p15.5-p15.4
chr11	4827728	10522050	DUP	0.626103426906853	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=LMO1|Tier1;DisruptL=MMP26;DisruptR=RNF141	yes	chr11p15.4
chr11	10522051	11283093	NEU	-0.152675827556769	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=RNF141;DisruptR=GALNT18	yes	chr11p15.4
chr11	11283094	12343815	DUP	0.563797535230402	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=GALNT18;DisruptR=MICAL2	yes	chr11p15.4-p15.3
chr11	12343816	27802356	NEU	-0.182702144964292	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MYOD1|Tier1,FANCF|Tier1;DisruptL=MICAL2;DisruptR=AC103796.1	yes	chr11p15.3-p14.1
chr11	27802357	29804998	DUP	0.5948544513172	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AC103796.1;DisruptR=AC107973.1	yes	chr11p14.1
chr11	29804999	36593149	NEU	-0.159104509966161	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=WT1|Tier1,LMO2|Tier1;DisruptL=AC107973.1;DisruptR=RAG2,RAG1	yes	chr11p14.1-p12
chr11	36593150	39290297	DUP	0.596432303302485	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=RAG2,RAG1;DisruptR=	yes	chr11p12
chr11	39290298	45539524	NEU	-0.206437655471976	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=EXT2|Tier1;DisruptL=;DisruptR=AC103855.2	yes	chr11p12-p11.2
chr11	45539525	48860163	DUP	0.538875722672056	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CREB3L1|Tier1,DDB2|Tier1;DisruptL=AC103855.2;DisruptR=	yes	chr11p11.2-p11.12
chr11	48860164	49740712	DUP	1.0357404046039	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV;COSMIC;DisruptL=;DisruptR=AC136759.1	yes	chr11p11.12
chr11	49740713	54537482	DUP	0.509063453203782	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=AC136759.1;DisruptR=	yes	chr11p11.12-q11
chr11	54537483	58828468	NEU	0.140157984831509	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CLP1|Tier2,CTNND1|Tier2;DisruptL=;DisruptR=	yes	chr11q11-q12.1
chr11	58828469	59869482	DUP	0.42454844963036	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr11q12.1
chr11	59869483	60292695	DUP	0.855801986455067	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=MS4A4A	yes	chr11q12.1-q12.2
chr11	60292696	65505149	NEU	-0.154420884297118	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FEN1|Tier2,MEN1|Tier1,MALAT1|Tier2,SDHAF2|Tier1;DisruptL=MS4A4A;DisruptR=MALAT1	yes	chr11q12.2-q13.1
chr11	65505150	67782059	DUP	0.238827526694619	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=MALAT1;DisruptR=	yes	chr11q13.1-q13.2
chr11	67782060	69098161	NEU	-0.186981778132212	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=TPCN2	yes	chr11q13.2-q13.3
chr11	69098162	69779346	DUP	2.89007232695178	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=CCND1|Tier1;DisruptL=TPCN2;DisruptR=	yes	chr11q13.3
chr11	69779347	70550613	DUP	1.94514381237447	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=SHANK2	yes	chr11q13.3-q13.4
chr11	70550614	74628578	NEU	-0.10704123658962	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=NUMA1|Tier1;DisruptL=SHANK2;DisruptR=POLD3	yes	chr11q13.4
chr11	74628579	78640469	DUP	0.629251675290376	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=POLD3;DisruptR=	yes	chr11q13.4-q14.1
chr11	78640470	80765005	NEU	-0.204111360555203	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr11q14.1
chr11	80765006	121197406	DEL	-0.742588026412558	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SDHD|Tier1,FAT3|Tier2,BIRC3|Tier1,POU2AF1|Tier1,PAFAH1B2|Tier1,DDX6|Tier1,BCL9L|Tier1,FOXR1|Tier2,EED|Tier2,MAML2|Tier1,ATM|Tier1,DDX10|Tier1,ZBTB16|Tier1,CBL|Tier1,ARHGEF12|Tier1,PICALM|Tier1,KMT2A|Tier1;DisruptL=;DisruptR=	no	chr11q14.1-q23.3
chr11	121197407	121473002	NEU	-0.190085440238974	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=SORL1	yes	chr11q23.3-q24.1
chr11	121473003	133550952	DEL	-0.794427596924045	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=KCNJ5|Tier1,FLI1|Tier1;DisruptL=SORL1;DisruptR=	yes	chr11q24.1-q25
chr11	133550953	135076522	DEL	-1.86613306522765	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr11q25
chr12	41087	56255706	NEU	-0.157389524529452	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=PTPN6|Tier2,CDKN1B|Tier1,HOXC13|Tier1,HOXC11|Tier1,KDM5A|Tier1,CCND2|Tier1,CHD4|Tier1,ZNF384|Tier1,KRAS|Tier1,COL2A1|Tier1,KMT2D|Tier1,PRPF40B|Tier2,SMARCD1|Tier1,ATF1|Tier1,ETV6|Tier1,ETNK1|Tier1,PPFIBP1|Tier1,ARID2|Tier1,ERBB3|Tier1,ERC1|Tier1;DisruptL=;DisruptR=ANKRD52	no	chr12p13.33-q13.3
chr12	56255707	61144893	DUP	0.848430805069277	bicseq2	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=	yes	chr12q13.3-q14.1
chr12	61144894	65713849	NEU	-0.135587345941363	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=WIF1|Tier1;DisruptL=;DisruptR=	yes	chr12q14.1-q14.3
chr12	65713850	67920515	DUP	2.44139144365597	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=HMGA2|Tier1;DisruptL=;DisruptR=	yes	chr12q14.3-q15
chr12	67920516	69782592	DUP	1.62102385421047	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MDM2|Tier1;DisruptL=;DisruptR=RAB3IP	yes	chr12q15
chr12	69782593	69869146	NEU	-0.137108731550078	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=RAB3IP;DisruptR=MYRFL	yes	chr12q15
chr12	69869147	71964313	DUP	1.48408085965061	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=PTPRB|Tier1;DisruptL=MYRFL;DisruptR=TPH2	yes	chr12q15-q21.1
chr12	71964314	72511836	DUP	2.10030099602226	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=TPH2;DisruptR=TRHDE	yes	chr12q21.1
chr12	72511837	112325530	NEU	-0.155317758686552	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=BTG1|Tier1,USP44|Tier2,SH2B3|Tier1,CHST11|Tier2,ALDH2|Tier2;DisruptL=TRHDE;DisruptR=HECTD4	no	chr12q21.1-q24.13
chr12	112325531	112386380	DUP	2.49382201982788	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HECTD4;DisruptR=	yes	chr12q24.13
chr12	112386381	125881076	NEU	-0.216937903518715	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=TBX3|Tier1,SETD1B|Tier2,ZCCHC8|Tier2,PTPN11|Tier1,HNF1A|Tier1,BCL7A|Tier1,CLIP1|Tier1,NCOR2|Tier1;DisruptL=;DisruptR=	yes	chr12q24.13-q24.32
chr12	125881077	133264924	NEU	0.134603433888147	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=POLE|Tier1;DisruptL=;DisruptR=	yes	chr12q24.32-q24.33
chr13	16000006	17402857	DUP	0.413858456291456	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr13p11.2-p11.1
chr13	17417970	23788156	DEL	-0.388880923335581	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ZNF198|Tier1;DisruptL=;DisruptR=MIPEP	yes	chr13p11.1-q12.12
chr13	23788157	24952567	NEU	0.0280325306149132	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=MIPEP;DisruptR=TPTE2P1	yes	chr13q12.12-q12.13
chr13	24952568	28880401	DUP	0.306840178420381	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CDX2|Tier1,FLT3|Tier1;DisruptL=TPTE2P1;DisruptR=MTUS2	yes	chr13q12.13-q12.3
chr13	28880402	68670604	DEL	-0.737249052158612	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CYSLTR2|Tier2,BRCA2|Tier1,LHFP|Tier2,FOXO1|Tier1,RB1|Tier1,NBEA|Tier2,LCP1|Tier2;DisruptL=MTUS2;DisruptR=	no	chr13q12.3-q21.33
chr13	68670605	68694604	DEL	-7.27778697445356	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV,1000G;DisruptL=;DisruptR=	yes	chr13q21.33
chr13	68694605	97331911	DEL	-0.718355363810263	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SOX21|Tier2,GPC5|Tier2;DisruptL=;DisruptR=MBNL2	no	chr13q21.33-q32.1
chr13	97331912	97689009	DEL	-1.65121254524351	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=MBNL2;DisruptR=	yes	chr13q32.1-q32.2
chr13	97689010	98509394	DEL	-0.732777840729469	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=STK24	yes	chr13q32.2
chr13	98509395	107327739	DUP	0.352985234227172	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ERCC5|Tier1;DisruptL=STK24;DisruptR=FAM155A	yes	chr13q32.2-q33.3
chr13	107327740	110418475	DUP	0.548762110285646	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=FAM155A;DisruptR=COL4A2	yes	chr13q33.3-q34
chr13	110418476	114354111	NEU	-0.214551134309649	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=COL4A2;DisruptR=	yes	chr13q34
chr14	16113916	20575158	NEU	0.125427330585452	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=CCNB1IP1|Tier1;DisruptL=;DisruptR=	yes	chr14p11.1-q11.2
chr14	20575159	21264197	DUP	0.676882755520223	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=HNRNPC	yes	chr14q11.2
chr14	21264198	41140316	NEU	0.0985654307308149	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=NKX2-1|Tier1,FOXA1|Tier1,ARHGAP5|Tier2,BAZ1A|Tier2;DisruptL=HNRNPC;DisruptR=	yes	chr14q11.2-q21.1
chr14	41140317	41200380	DEL	-7.02527465311802	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr14q21.1
chr14	41200381	91109806	NEU	0.08582521082306	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SIX1|Tier1,NIN|Tier1,KTN1|Tier1,MAX|Tier1,HIF1A|Tier1,TSHR|Tier1,RAD51B|Tier1,GPHN|Tier1;DisruptL=;DisruptR=DGLUCY	no	chr14q21.1-q32.11
chr14	91109807	91493434	DUP	0.594386161391343	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=DGLUCY;DisruptR=PPP4R3A	yes	chr14q32.11-q32.12
chr14	91493435	104242963	NEU	0.00913317631554553	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=TCL1A|Tier1,DICER1|Tier1,TRIP11|Tier1,GOLGA5|Tier1,BCL11B|Tier1,HSP90AA1|Tier1;DisruptL=PPP4R3A;DisruptR=AL590079.1	yes	chr14q32.12-q32.33
chr14	104242964	106883618	DUP	1.74719560247174	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=AKT1|Tier1;DisruptL=AL590079.1;DisruptR=	yes	chr14q32.33
chr15	17083473	56746778	NEU	-0.12815989079006	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=NUTM1|Tier1,BUB1B|Tier1,KNSTRN|Tier2,B2M|Tier1,CASC5|Tier1,USP8|Tier1,MYO5A|Tier1;DisruptL=;DisruptR=AC090517.4	no	chr15p11.2-q21.3
chr15	56746779	65078451	DUP	0.603666040423654	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=TCF12|Tier1;DisruptL=AC090517.4;DisruptR=	yes	chr15q21.3-q22.31
chr15	65078452	72000143	NEU	0.185150194647658	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MAP2K1|Tier1,SMAD3|Tier1;DisruptL=;DisruptR=AC022872.1,MYO9A	yes	chr15q22.31-q23
chr15	72000144	72362589	DUP	0.835378970747134	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AC022872.1,MYO9A;DisruptR=AC009690.1,HEXA	yes	chr15q23
chr15	72362590	101981087	NEU	0.140104139641511	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FES|Tier1,PML|Tier1,POLG|Tier2,IDH2|Tier1,BLM|Tier1,CRTC3|Tier1,CHD2|Tier2,NTRK3|Tier1;DisruptL=AC009690.1,HEXA;DisruptR=	no	chr15q23-q26.3
chr16	10005	13285377	NEU	-0.0972411620955463	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_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=U91319.1	yes	chr16p13.3-p13.12
chr16	13285378	34502581	DUP	0.309295386296136	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FUS|Tier1,ERCC4|Tier1,PALB2|Tier1,IL21R|Tier1,MYH11|Tier1,PRKCB|Tier2;DisruptL=U91319.1;DisruptR=	no	chr16p13.12-p11.2
chr16	34596149	90226217	NEU	-0.183269324454687	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=MAF|Tier1,CYLD|Tier1,HERPUD1|Tier1,CDH11|Tier1,CBFB|Tier1,RFWD3|Tier2,CBFA2T3|Tier1,CTCF|Tier1,CDH1|Tier1,ZFHX3|Tier1,FANCA|Tier1;DisruptL=;DisruptR=	no	chr16p11.2-q24.3
chr17	168977	21658447	DUP	0.214418694213613	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=TP53|Tier1,YWHAE|Tier1,USP6|Tier1,PER1|Tier1,FLCN|Tier1,RABEP1|Tier1,GAS7|Tier1,MAP2K4|Tier1,NCOR1|Tier1,SPECC1|Tier2;DisruptL=DOC2B;DisruptR=	no	chr17p13.3-p11.2
chr17	22044138	34345057	DEL	-0.258870784704639	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=NF1|Tier1,SUZ12|Tier1;DisruptL=;DisruptR=	yes	chr17p11.2-q12
chr17	34345058	36041470	DUP	0.245656729687892	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=TAF15|Tier1;DisruptL=;DisruptR=	yes	chr17q12
chr17	36041471	39577425	DEL	-0.703221895684216	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MLLT6|Tier1,LASP1|Tier1,CDK12|Tier1;DisruptL=;DisruptR=	yes	chr17q12
chr17	39577426	39805109	DUP	0.247745681977206	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ERBB2|Tier1;DisruptL=;DisruptR=IKZF3	yes	chr17q12-q21.1
chr17	39805110	43301596	DEL	-0.719491153272787	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CCR7|Tier2,RARA|Tier1,SMARCE1|Tier1,STAT5B|Tier1,STAT3|Tier1,BRCA1|Tier1;DisruptL=IKZF3;DisruptR=LINC00854	yes	chr17q21.1-q21.31
chr17	43301597	47874912	NEU	0.166881743018636	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ETV4|Tier1;DisruptL=LINC00854;DisruptR=	yes	chr17q21.31-q21.32
chr17	47874913	48072289	DUP	1.19196567963052	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=CBX1	yes	chr17q21.32
chr17	48072290	55607901	DUP	0.201050538343134	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SPOP|Tier1,KAT7|Tier2,COL1A1|Tier1,HLF|Tier1;DisruptL=CBX1;DisruptR=	yes	chr17q21.32-q22
chr17	55607902	59518846	DUP	0.812236620980936	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=RNF43|Tier1,MSI2|Tier1;DisruptL=;DisruptR=LINC01476	yes	chr17q22-q23.1
chr17	59518847	67102559	NEU	-0.141801359846449	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=PPM1D|Tier1,CD79B|Tier1,DDX5|Tier1,CLTC|Tier1,BRIP1|Tier1,AXIN2|Tier1;DisruptL=LINC01476;DisruptR=HELZ	yes	chr17q23.1-q24.2
chr17	67102560	83247341	DUP	0.787702316296601	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=H3F3B|Tier1,SRSF2|Tier1,CANT1|Tier1,PRKAR1A|Tier1,ASPSCR1|Tier1,SEPT9|Tier2,RNF213|Tier1;DisruptL=HELZ;DisruptR=	yes	chr17q24.2-q25.3
chr18	10010	276979	DUP	0.224764366707452	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV;COSMIC;DisruptL=;DisruptR=	yes	chr18p11.32
chr18	276980	3047103	DUP	0.952586276905374	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV;COSMIC;DisruptL=;DisruptR=	yes	chr18p11.32-p11.31
chr18	3047104	7909753	DUP	1.14749850928036	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=PTPRM	yes	chr18p11.31-p11.23
chr18	7909754	11293917	DUP	1.47094933718664	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=PTPRM;DisruptR=	yes	chr18p11.23-p11.21
chr18	11293918	11707457	DUP	1.08251253822977	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=GNAL	yes	chr18p11.21
chr18	11707458	20553041	NEU	0.14934991801601	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=GNAL;DisruptR=	yes	chr18p11.21-q11.1
chr18	20553042	23307595	DEL	-0.260022850608005	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=TMEM241	yes	chr18q11.1-q11.2
chr18	23307596	23971374	DUP	1.23007885798867	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=TMEM241;DisruptR=AC010754.1	yes	chr18q11.2
chr18	23971375	24279487	DUP	0.562228939989109	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AC010754.1;DisruptR=OSBPL1A	yes	chr18q11.2
chr18	24279488	24684888	DEL	-0.265924835949798	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=OSBPL1A;DisruptR=	yes	chr18q11.2
chr18	24684889	30130550	DEL	-0.700415612908919	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SS18|Tier1,ZNF521|Tier1;DisruptL=;DisruptR=	yes	chr18q11.2-q12.1
chr18	30130551	40264437	DEL	-0.895137865908886	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr18q12.1-q12.3
chr18	40264438	49182019	DEL	-0.288833589312673	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SMAD2|Tier1,SETBP1|Tier1;DisruptL=;DisruptR=DYM	yes	chr18q12.3-q21.1
chr18	49182020	57412429	DEL	-0.928835257749845	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SMAD4|Tier1,DCC|Tier2;DisruptL=DYM;DisruptR=	yes	chr18q21.1-q21.31
chr18	57412430	59280727	DEL	-0.488978645192613	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MALT1|Tier1;DisruptL=;DisruptR=CPLX4	yes	chr18q21.31-q21.32
chr18	59280728	61626359	DEL	-0.879591647580495	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=CPLX4;DisruptR=AC105094.2	yes	chr18q21.32-q21.33
chr18	61626360	63805004	DUP	0.274514955512614	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=KDSR|Tier1,BCL2|Tier1;DisruptL=AC105094.2;DisruptR=SERPINB7	yes	chr18q21.33
chr18	63805005	67194596	DUP	0.490842908332744	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV;COSMIC;DisruptL=SERPINB7;DisruptR=	yes	chr18q21.33-q22.1
chr18	67194597	73990268	NEU	0.181506644124724	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=AC090125.1	yes	chr18q22.1-q22.3
chr18	73990269	80263172	DUP	0.42601223553199	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=AC090125.1;DisruptR=	yes	chr18q22.3-q23
chr19	90733	12858960	NEU	-0.188059575981536	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=FSTL3|Tier1,CD209|Tier2,KEAP1|Tier1,STK11|Tier1,TCF3|Tier1,GNA11|Tier1,MAP2K2|Tier1,SH3GL1|Tier1,MLLT1|Tier1,MUC16|Tier2,VAV1|Tier2,DNM2|Tier1,SMARCA4|Tier1;DisruptL=;DisruptR=HOOK2,MAST1	yes	chr19p13.3-p13.13
chr19	12858961	12880012	DEL	-7.02961844226818	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=HOOK2,MAST1;DisruptR=DNASE2	yes	chr19p13.13
chr19	12880013	14687523	NEU	-0.15905420673502	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=LYL1|Tier1,CALR|Tier1,PRKACA|Tier1,DNAJB1|Tier1;DisruptL=DNASE2;DisruptR=ADGRE3	yes	chr19p13.13-p13.12
chr19	14687524	15684658	DUP	1.93166273785793	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=BRD4|Tier1;DisruptL=ADGRE3;DisruptR=CYP4F12	yes	chr19p13.12
chr19	15684659	20137237	NEU	-0.0235176657070789	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=TPM4|Tier1,JAK3|Tier1,ELL|Tier1,CRTC1|Tier1;DisruptL=CYP4F12;DisruptR=AC011447.2,AC011447.3	yes	chr19p13.12-p12
chr19	20137238	20502055	DUP	0.888369446569572	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=DGV;DisruptL=AC011447.2,AC011447.3;DisruptR=AC008554.1	yes	chr19p12
chr19	20502056	23543309	NEU	-0.187574495615049	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ZNF429|Tier2;DisruptL=AC008554.1;DisruptR=ZNF675	yes	chr19p12
chr19	23543310	24014084	DUP	0.34560673204819	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ZNF675;DisruptR=	yes	chr19p12
chr19	24014085	58607515	NEU	-0.109568975180704	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CEBPA|Tier1,BCL3|Tier1,BCL2L12|Tier2,KLK2|Tier1,TFPT|Tier2,CCNE1|Tier1,CD79A|Tier1,CIC|Tier1,CBLC|Tier1,ERCC2|Tier1,BAX|Tier1,POLD1|Tier1,PPP2R1A|Tier1,ZNF331|Tier1,CNOT3|Tier1,CEP89|Tier2,LSM14A|Tier2,AKT2|Tier1;DisruptL=;DisruptR=	no	chr19p12-q13.43
chr20	67260	8765219	DUP	0.529478271316147	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SIRPA|Tier2;DisruptL=;DisruptR=PLCB1	yes	chr20p13-p12.3
chr20	8765220	21885644	DUP	0.785507120814987	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=CRNKL1|Tier2;DisruptL=PLCB1;DisruptR=	yes	chr20p12.3-p11.22
chr20	21885645	28506070	DUP	0.929613901184557	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=	yes	chr20p11.22-q11.1
chr20	29339193	30761316	NEU	0.138922175893282	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;DisruptL=;DisruptR=	yes	chr20q11.1-q11.21
chr20	31245066	31539738	DUP	1.20309260495044	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=HM13	yes	chr20q11.21
chr20	31539739	34230620	DUP	1.84905715053213	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=ASXL1|Tier1;DisruptL=HM13;DisruptR=ASIP	yes	chr20q11.21-q11.22
chr20	34230621	37368800	DUP	1.22169669829972	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=ASIP;DisruptR=SRC	yes	chr20q11.22-q11.23
chr20	37368801	39349450	DUP	0.997105132787848	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SRC|Tier1;DisruptL=SRC;DisruptR=	yes	chr20q11.23-q12
chr20	39349451	64334067	NEU	0.180689310414981	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=MAFB|Tier1,TOP1|Tier1,SDC4|Tier1,SALL4|Tier1,GNAS|Tier1,SS18L1|Tier1,PTK6|Tier1,PLCG1|Tier1,NFATC2|Tier1,PTPRT|Tier1;DisruptL=;DisruptR=	no	chr20q12-q13.33
chr21	12966568	14697622	DUP	1.23576887738893	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr21q11.1-q11.2
chr21	14697623	15873584	DUP	1.54454337660412	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=USP25	yes	chr21q11.2-q21.1
chr21	15873585	17474345	DUP	0.280765047852804	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=USP25;DisruptR=	yes	chr21q21.1
chr21	17474346	17986205	DUP	1.60120346183876	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=CHODL	yes	chr21q21.1
chr21	17986206	18481759	DUP	0.479712331758348	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=CHODL;DisruptR=TMPRSS15,AL109763.1	yes	chr21q21.1
chr21	18481760	20113683	NEU	0.0964684063434238	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=TMPRSS15,AL109763.1;DisruptR=	yes	chr21q21.1
chr21	20113684	26634790	NEU	-0.146535772217581	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr21q21.1-q21.3
chr21	26634791	31947284	DEL	-0.632041491924216	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=HUNK	yes	chr21q21.3-q22.11
chr21	31947285	32738934	DUP	0.73200014588437	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=HUNK;DisruptR=PAXBP1-AS1,PAXBP1	yes	chr21q22.11
chr21	32738935	34714566	DUP	0.273787877392145	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=OLIG2|Tier1;DisruptL=PAXBP1-AS1,PAXBP1;DisruptR=CLIC6	yes	chr21q22.11-q22.12
chr21	34714567	34819639	DEL	-1.2176809950332	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=RUNX1|Tier1;DisruptL=CLIC6;DisruptR=RUNX1	yes	chr21q22.12
chr21	34819640	34847754	DEL	-7.77384007813264	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=RUNX1|Tier1;DisruptL=RUNX1;DisruptR=RUNX1	yes	chr21q22.12
chr21	34847755	40764259	DEL	-0.479745190157	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=RUNX1|Tier1,ERG|Tier1;DisruptL=RUNX1;DisruptR=DSCAM	yes	chr21q22.12-q22.2
chr21	40764260	41078298	DUP	1.13873912071532	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=DSCAM;DisruptR=	yes	chr21q22.2
chr21	41078299	41822925	DEL	-0.338259073729751	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=TMPRSS2|Tier1;DisruptL=;DisruptR=PRDM15	yes	chr21q22.2-q22.3
chr21	41822926	42103808	DUP	1.11596713845197	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=PRDM15;DisruptR=UMODL1-AS1,UMODL1	yes	chr21q22.3
chr21	42103809	44064549	NEU	-0.084248054186992	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=U2AF1|Tier1;DisruptL=UMODL1-AS1,UMODL1;DisruptR=TRAPPC10	yes	chr21q22.3
chr21	44064550	46107841	DUP	1.21527417213891	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=TRAPPC10;DisruptR=COL6A2	yes	chr21q22.3
chr21	46107842	46699872	NEU	-0.0510103275160563	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=COL6A2;DisruptR=	yes	chr21q22.3
chr22	10514978	23763093	DUP	0.869090727384451	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;Cancer_census=SEPT5|Tier2,DGCR8|Tier2,LZTR1|Tier1,MAPK1|Tier1,CLTCL1|Tier1,BCR|Tier1;DisruptL=;DisruptR=C22orf15	yes	chr22p11.2-q11.23
chr22	23763094	29406094	DUP	1.11619692049049	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=SMARCB1|Tier1,ZNRF3|Tier2,EWSR1|Tier1,MN1|Tier1,CHEK2|Tier1;DisruptL=C22orf15;DisruptR=AP1B1	yes	chr22q11.23-q12.2
chr22	29406279	46073918	DUP	0.699067874413906	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;Cancer_census=APOBEC3B|Tier1,ZNF278|Tier1,ISX|Tier2,PDGFB|Tier1,MKL1|Tier1,NF2|Tier1,MYH9|Tier1,EP300|Tier1;DisruptL=AP1B1;DisruptR=MIRLET7BHG	yes	chr22q12.2-q13.31
chr22	46073919	46234133	DUP	1.25287520547635	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=MIRLET7BHG;DisruptR=PPARA	yes	chr22q13.31
chr22	46234134	50808368	DUP	0.627401751248704	bicseq2	HCC-1143-NovaSeq_80--HCC-1143BL-NovaSeq_40	known=;COSMIC;DisruptL=PPARA;DisruptR=	yes	chr22q13.31-q13.33