#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	31283107	DUP	0.212150407722613	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=P2RY8|Tier1,CRLF2|Tier1,ZRSR2|Tier1,EIF1AX|Tier2;DisruptL=;DisruptR=DMD	no	chrXp22.33-p21.2
chrX	31283108	32080447	DEL	-0.634975285535188	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;DisruptL=DMD;DisruptR=DMD	yes	chrXp21.2-p21.1
chrX	32080448	32183115	DEL	-2.73312207080245	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;DisruptL=DMD;DisruptR=DMD	yes	chrXp21.1
chrX	32183116	156030795	DUP	0.293272004625558	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=ARAF|Tier2,SSX1|Tier1,WAS|Tier1,FOXO4|Tier1,ZMYM3|Tier2,NONO|Tier1,IRS4|Tier1,DCAF12L2|Tier2,RPL10|Tier1,MTCP1|Tier1,FAM47C|Tier2,BCOR|Tier1,DDX3X|Tier1,SSX4|Tier1,GATA1|Tier1,TFE3|Tier1,SSX2|Tier1,SMC1A|Tier2,AMER1|Tier1,MSN|Tier1,MED12|Tier1,BTK|Tier1,STAG2|Tier1,ELF4|Tier1,PHF6|Tier1,ATP2B3|Tier1,FLNA|Tier2,KDM5C|Tier1,AR|Tier1,SEPT6|Tier2,GPC3|Tier1,KDM6A|Tier1,RBM10|Tier1,ATRX|Tier1,BCORL1|Tier1;DisruptL=DMD;DisruptR=	no	chrXp21.1-q28
chr1	791595	86871338	NEU	-0.105979242048474	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=TNFRSF14|Tier1,ID3|Tier2,MDS2|Tier2,MYCL|Tier1,TAL1|Tier1,JUN|Tier1,BCL10|Tier1,SKI|Tier2,RPL22|Tier1,CASP9|Tier2,PAX7|Tier1,LCK|Tier1,SFPQ|Tier1,THRAP3|Tier2,CSF3R|Tier1,MPL|Tier1,MUTYH|Tier1,STIL|Tier1,CDKN2C|Tier1,FUBP1|Tier1,MTOR|Tier1,PRDM2|Tier2,SPEN|Tier1,SDHB|Tier1,ARHGEF10L|Tier2,ARID1A|Tier1,JAK1|Tier1,PRDM16|Tier1,CAMTA1|Tier1,EPS15|Tier1;DisruptL=AL669831.3,AL669831.5;DisruptR=SELENOF	no	chr1p36.33-p22.3
chr1	86871339	125079644	DEL	-0.655776203973258	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=RPL5|Tier1,RBM15|Tier1,NRAS|Tier1,FAM46C|Tier1,TRIM33|Tier1,NOTCH2|Tier1,ATP1A1|Tier1;DisruptL=SELENOF;DisruptR=	no	chr1p22.3-q11
chr1	143541117	144101334	DEL	-5.66802844543947	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;DisruptL=;DisruptR=	yes	chr1q21.1
chr1	144101335	248576186	DUP	0.309142609426312	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=MLLT11|Tier1,S100A7|Tier2,SLC45A3|Tier1,BCL9|Tier1,TPM3|Tier1,LMNA|Tier1,PRCC|Tier1,NTRK1|Tier1,FCRL4|Tier1,FCGR2B|Tier1,DDR2|Tier1,PRRX1|Tier1,ABL2|Tier1,TPR|Tier1,ELF3|Tier2,MDM4|Tier1,ELK4|Tier1,H3F3A|Tier1,FH|Tier1,ARNT|Tier1,SDHC|Tier1,CDC73|Tier1,PTPRC|Tier1,AKT3|Tier2,PDE4DIP|Tier1,MUC1|Tier1,PBX1|Tier1,RGS7|Tier2;DisruptL=;DisruptR=	no	chr1q21.1-q44
chr1	248576187	248634718	DEL	-8.38045837152303	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=DGV;COSMIC;DisruptL=;DisruptR=OR2T11	yes	chr1q44
chr1	248634719	248946322	DUP	0.279329059782231	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=DGV;DisruptL=OR2T11;DisruptR=	yes	chr1q44
chr2	10005	242183395	NEU	-0.0802727168451644	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=MYCN|Tier1,PCBP1|Tier2,CXCR4|Tier1,HOXD13|Tier1,HOXD11|Tier1,FEV|Tier1,ACKR3|Tier1,C2orf44|Tier1,NCOA1|Tier1,ASXL2|Tier2,SIX2|Tier2,EPAS1|Tier1,MSH6|Tier1,FBXO11|Tier1,BCL11A|Tier1,REL|Tier1,XPO1|Tier1,DCTN1|Tier1,TMEM127|Tier1,RANBP2|Tier1,ACVR1|Tier1,NFE2L2|Tier1,CASP8|Tier1,CD28|Tier2,CREB1|Tier1,IDH1|Tier1,BARD1|Tier1,ATIC|Tier1,ACSL3|Tier1,DNMT3A|Tier1,STRN|Tier1,EML4|Tier1,MSH2|Tier1,RGPD3|Tier2,ERCC3|Tier1,COL3A1|Tier2,SF3B1|Tier1,CUL3|Tier2,ALK|Tier1,BIRC6|Tier2,AFF3|Tier1,PAX8|Tier1,LRP1B|Tier1,ACVR2A|Tier1,ITGAV|Tier2,PMS1|Tier2,ERBB4|Tier1,PAX3|Tier1;DisruptL=;DisruptR=	no	chr2p25.3-q37.3
chr3	10005	24523547	DEL	-0.661752312646228	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=VHL|Tier1,PPARG|Tier1,RAF1|Tier1,SRGAP3|Tier2,FANCD2|Tier1,XPC|Tier1,FBLN2|Tier2;DisruptL=;DisruptR=THRB-AS1	no	chr3p26.3-p24.2
chr3	24523548	25359526	DUP	1.646329284566	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;DisruptL=THRB-AS1;DisruptR=RARB	yes	chr3p24.2
chr3	25359527	26410780	DUP	1.30384986703151	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;DisruptL=RARB;DisruptR=	yes	chr3p24.2-p24.1
chr3	26410781	26622388	DUP	1.92105999824238	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;DisruptL=;DisruptR=AC099754.1	yes	chr3p24.1
chr3	26622389	198139690	DUP	0.326827549174769	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=CCR4|Tier2,MYD88|Tier1,BAP1|Tier1,FOXL2|Tier1,SOX2|Tier1,EIF4A2|Tier1,MLH1|Tier1,CTNNB1|Tier1,NCKIPSD|Tier2,RHOA|Tier1,MITF|Tier1,TFG|Tier1,GATA2|Tier1,RPN1|Tier1,CNBP|Tier1,GMPS|Tier2,MECOM|Tier1,TBL1XR1|Tier1,PIK3CA|Tier1,ETV5|Tier1,BCL6|Tier1,MUC4|Tier2,TFRC|Tier2,TGFBR2|Tier1,SETD2|Tier1,PBRM1|Tier1,CACNA1D|Tier1,FOXP1|Tier1,CBLB|Tier1,POLQ|Tier1,STAG1|Tier2,PIK3CB|Tier1,ATR|Tier1,WWTR1|Tier1,MLF1|Tier1,MAP3K13|Tier1,IGF2BP2|Tier2,MB21D2|Tier2,FHIT|Tier1,ROBO2|Tier2,EPHA3|Tier2,LPP|Tier1,TP63|Tier1;DisruptL=AC099754.1;DisruptR=	no	chr3p24.1-q29
chr4	10011	51107080	DEL	-0.642362598704679	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=RHOH|Tier1,FGFR3|Tier1,SLC34A2|Tier1,PHOX2B|Tier1,TEC|Tier2,WHSC1|Tier1,N4BP2|Tier2;DisruptL=;DisruptR=	no	chr4p16.3-q11
chr4	51108134	190106211	DUP	0.271234294355616	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=DUX4L1|Tier2,FIP1L1|Tier1,CHIC2|Tier2,KIT|Tier1,KDR|Tier1,IL2|Tier1,FBXW7|Tier1,CASP3|Tier2,PDGFRA|Tier1,PTPN13|Tier1,RAP1GDS1|Tier1,TET2|Tier1,LEF1|Tier1,FAT4|Tier1,AFF1|Tier1,FAT1|Tier1;DisruptL=;DisruptR=	no	chr4q11-q35.2
chr5	11484	17517515	DEL	-0.65021849107364	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=SDHA|Tier1,TERT|Tier1,CTNND2|Tier2;DisruptL=;DisruptR=	yes	chr5p15.33-p15.1
chr5	17517516	17645389	DEL	-6.78596357095277	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;DisruptL=;DisruptR=	yes	chr5p15.1
chr5	17645390	28787898	DEL	-0.675284258053215	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=CDH10|Tier2;DisruptL=;DisruptR=AC008825.1	yes	chr5p15.1-p14.1
chr5	28787899	28962927	DEL	-1.80555857255747	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=DGV;DisruptL=AC008825.1;DisruptR=	yes	chr5p14.1-p13.3
chr5	28962928	180949083	DEL	-0.659720178405728	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=RAD17|Tier2,IL7R|Tier1,LIFR|Tier1,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,DROSHA|Tier1,NSD1|Tier1;DisruptL=;DisruptR=BTNL8	no	chr5p13.3-q35.3
chr5	180949084	181003477	DEL	-7.53775769717339	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=DGV,1000G;COSMIC;DisruptL=BTNL8;DisruptR=BTNL3	yes	chr5q35.3
chr5	181003478	181449255	DEL	-0.644082989598171	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;DisruptL=BTNL3;DisruptR=	yes	chr5q35.3
chr6	89830	64637568	DUP	0.31905432861792	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=HIST1H3B|Tier1,HIST1H4I|Tier1,HLA-A|Tier1,POU5F1|Tier1,DAXX|Tier1,CDKN1A|Tier2,PIM1|Tier1,TFEB|Tier1,CCND3|Tier1,NFKBIE|Tier1,DEK|Tier1,TRIM27|Tier1,HMGA1|Tier1,FANCE|Tier1,SRSF3|Tier1,HSP90AB1|Tier1,IRF4|Tier1,BMP5|Tier2;DisruptL=;DisruptR=EYS	no	chr6p25.3-q12
chr6	64637569	170740360	NEU	-0.097035900002482	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=SGK1|Tier2,PRDM1|Tier1,MYB|Tier1,BCLAF1|Tier2,TNFAIP3|Tier1,ECT2L|Tier2,EZR|Tier1,FGFR1OP|Tier1,CCNC|Tier2,FOXO3|Tier1,ROS1|Tier1,GOPC|Tier1,RSPO3|Tier1,PTPRK|Tier1,ARID1B|Tier1,QKI|Tier1,MLLT4|Tier1,EPHA7|Tier2,ESR1|Tier1;DisruptL=EYS;DisruptR=	no	chr6q12-q27
chr7	16339	126105997	DUP	0.332741529447203	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-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,ZNF479|Tier2,SBDS|Tier1,POT1|Tier1,JAZF1|Tier2,EGFR|Tier1,ELN|Tier2,HIP1|Tier1,GRM3|Tier2,AKAP9|Tier2,CDK6|Tier1,TRRAP|Tier1,CUX1|Tier1,MET|Tier1,IKZF1|Tier1;DisruptL=AC215522.3;DisruptR=	no	chr7p22.3-q31.33
chr7	126105998	126458399	DEL	-0.616503766024273	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=GRM8	yes	chr7q31.33
chr7	126458400	144214183	DUP	0.916888317412011	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=SMO|Tier1,KIAA1549|Tier2,FAM131B|Tier2,CREB3L2|Tier1,TRIM24|Tier1,BRAF|Tier1,SND1|Tier1;DisruptL=GRM8;DisruptR=AC004889.1	yes	chr7q31.33-q35
chr7	144214184	151049592	DUP	0.344834630806323	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=EZH2|Tier1,CNTNAP2|Tier2;DisruptL=AC004889.1;DisruptR=ASIC3	yes	chr7q35-q36.1
chr7	151049593	159335873	DEL	-0.653840838244903	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=MNX1|Tier2,KMT2C|Tier1;DisruptL=ASIC3;DisruptR=	yes	chr7q36.1-q36.3
chr8	71162	145078494	DUP	0.200534411080589	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=TCEA1|Tier1,PLAG1|Tier1,CHCHD7|Tier1,HEY1|Tier1,COX6C|Tier2,MYC|Tier1,RECQL4|Tier1,ARHGEF10|Tier2,LEPROTL1|Tier2,WHSC1L1|Tier1,FGFR1|Tier1,IKBKB|Tier1,NBN|Tier1,CDH17|Tier2,PABPC1|Tier2,EIF3E|Tier1,RAD21|Tier1,NDRG1|Tier1,PCM1|Tier1,WRN|Tier1,NRG1|Tier1,ANK1|Tier2,NCOA2|Tier1,RUNX1T1|Tier1,UBR5|Tier1,EXT1|Tier1,FAM135B|Tier2,HOOK3|Tier1,PREX2|Tier1,CNBD1|Tier2,RSPO2|Tier1,CSMD3|Tier2;DisruptL=;DisruptR=	no	chr8p23.3-q24.3
chr9	10000	30338983	DEL	-0.672565442985919	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=CD274|Tier1,PDCD1LG2|Tier1,PSIP1|Tier1,CDKN2A|Tier1,JAK2|Tier1,NFIB|Tier1,MLLT3|Tier1,PTPRD|Tier2;DisruptL=;DisruptR=	no	chr9p24.3-p21.1
chr9	30338984	138313848	DUP	0.286655145366919	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;Cancer_census=OMD|Tier2,KLF4|Tier1,TAL2|Tier1,SET|Tier1,FANCG|Tier1,SYK|Tier1,PTCH1|Tier1,XPA|Tier1,NR4A3|Tier1,ABL1|Tier1,RALGDS|Tier2,BRD3|Tier1,NOTCH1|Tier1,PAX5|Tier1,GNAQ|Tier1,WNK2|Tier2,FANCC|Tier1,TNC|Tier2,CNTRL|Tier1,PPP6C|Tier1,NUP214|Tier1,TSC1|Tier1,FNBP1|Tier2;DisruptL=;DisruptR=	no	chr9p21.1-q34.3
chr10	10287	7592026	DEL	-0.641893674627577	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=LARP4B|Tier2,KLF6|Tier1;DisruptL=;DisruptR=ITIH5	yes	chr10p15.3-p14
chr10	7592027	33097469	NEU	-0.134369841935669	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=GATA3|Tier1,ABI1|Tier1,KIF5B|Tier1,MLLT10|Tier1,ZEB1|Tier2;DisruptL=ITIH5;DisruptR=AL121748.1	no	chr10p14-p11.22
chr10	33097470	133787316	DEL	-0.653030889547254	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=NCOA4|Tier1,TLX1|Tier1,PRF1|Tier1,NUTM2B|Tier1,NUTM2A|Tier1,CYP2C8|Tier2,NFKB2|Tier1,RET|Tier1,A1CF|Tier2,CCDC6|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=AL121748.1;DisruptR=	no	chr10p11.22-q26.3
chr11	128355	81074540	NEU	-0.0653632116482814	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=HRAS|Tier1,MYOD1|Tier1,FANCF|Tier1,CLP1|Tier2,FEN1|Tier2,MEN1|Tier1,MALAT1|Tier2,NUP98|Tier1,WT1|Tier1,LMO2|Tier1,CREB3L1|Tier1,DDB2|Tier1,SDHAF2|Tier1,CCND1|Tier1,NUMA1|Tier1,CARS|Tier1,LMO1|Tier1,EXT2|Tier1,CTNND1|Tier2;DisruptL=LINC01001;DisruptR=	no	chr11p15.5-q14.1
chr11	81074541	81382721	DEL	-0.992429851910066	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr11q14.1
chr11	81382722	135076522	NEU	-0.124240029060578	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=SDHD|Tier1,KCNJ5|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,FLI1|Tier1,PICALM|Tier1,KMT2A|Tier1;DisruptL=;DisruptR=	no	chr11q14.1-q25
chr12	41087	133264924	NEU	-0.0781714487861296	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=PTPN6|Tier2,CDKN1B|Tier1,HOXC13|Tier1,HOXC11|Tier1,NAB2|Tier1,GLI1|Tier2,DDIT3|Tier1,CDK4|Tier1,BTG1|Tier1,TBX3|Tier1,SETD1B|Tier2,KDM5A|Tier1,CCND2|Tier1,CHD4|Tier1,ZNF384|Tier1,KRAS|Tier1,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,ETV6|Tier1,ETNK1|Tier1,PPFIBP1|Tier1,ARID2|Tier1,ERBB3|Tier1,HMGA2|Tier1,MDM2|Tier1,CHST11|Tier2,ALDH2|Tier2,PTPN11|Tier1,HNF1A|Tier1,BCL7A|Tier1,CLIP1|Tier1,NCOR2|Tier1,POLE|Tier1,ERC1|Tier1;DisruptL=;DisruptR=	no	chr12p13.33-q24.33
chr13	16000006	114354111	NEU	0.0969691116988634	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=CYSLTR2|Tier2,SOX21|Tier2,CDX2|Tier1,ERCC5|Tier1,ZNF198|Tier1,FLT3|Tier1,BRCA2|Tier1,LHFP|Tier2,FOXO1|Tier1,RB1|Tier1,NBEA|Tier2,LCP1|Tier2,GPC5|Tier2;DisruptL=;DisruptR=	no	chr13p11.2-q34
chr14	18670975	18697902	DEL	-6.5474531623904	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=DGV;DisruptL=;DisruptR=	yes	chr14q11.2
chr14	18697903	106883618	NEU	-0.070986068777406	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=NKX2-1|Tier1,FOXA1|Tier1,SIX1|Tier1,TCL1A|Tier1,NIN|Tier1,KTN1|Tier1,MAX|Tier1,DICER1|Tier1,AKT1|Tier1,CCNB1IP1|Tier1,ARHGAP5|Tier2,BAZ1A|Tier2,HIF1A|Tier1,TSHR|Tier1,TRIP11|Tier1,GOLGA5|Tier1,BCL11B|Tier1,HSP90AA1|Tier1,RAD51B|Tier1,GPHN|Tier1;DisruptL=;DisruptR=	no	chr14q11.2-q32.33
chr15	17083473	23747520	DUP	0.317808488896132	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;DisruptL=;DisruptR=	yes	chr15p11.2-q11.2
chr15	23747521	84142010	DEL	-0.640549033540064	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=NUTM1|Tier1,BUB1B|Tier1,KNSTRN|Tier2,B2M|Tier1,PML|Tier1,CASC5|Tier1,USP8|Tier1,TCF12|Tier1,MAP2K1|Tier1,MYO5A|Tier1,SMAD3|Tier1;DisruptL=;DisruptR=	no	chr15q11.2-q25.2
chr15	84142011	101981087	DUP	0.336453515265511	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=FES|Tier1,POLG|Tier2,IDH2|Tier1,BLM|Tier1,CRTC3|Tier1,CHD2|Tier2,NTRK3|Tier1;DisruptL=;DisruptR=	yes	chr15q25.2-q26.3
chr16	10005	34502581	NEU	0.174008748355448	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=TRAF7|Tier1,SOCS1|Tier1,RMI2|Tier1,TNFRSF17|Tier1,FUS|Tier1,AXIN1|Tier1,TSC2|Tier1,RUNDC2A|Tier2,ERCC4|Tier1,PALB2|Tier1,IL21R|Tier1,CREBBP|Tier1,GRIN2A|Tier1,CIITA|Tier1,NTHL1|Tier2,MYH11|Tier1,PRKCB|Tier2;DisruptL=;DisruptR=	no	chr16p13.3-p11.2
chr16	34596149	58590672	DEL	-0.630396351965899	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;Cancer_census=CYLD|Tier1,HERPUD1|Tier1;DisruptL=;DisruptR=CNOT1	no	chr16p11.2-q21
chr16	58590673	58629425	DEL	-4.95568604785239	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;DisruptL=CNOT1;DisruptR=CNOT1	yes	chr16q21
chr16	58629426	90226217	DEL	-0.618641891592847	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=MAF|Tier1,CDH11|Tier1,CBFB|Tier1,RFWD3|Tier2,CBFA2T3|Tier1,CTCF|Tier1,CDH1|Tier1,ZFHX3|Tier1,FANCA|Tier1;DisruptL=CNOT1;DisruptR=	no	chr16q21-q24.3
chr17	168977	83247341	NEU	0.0167947587360958	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=TP53|Tier1,CCR7|Tier2,H3F3B|Tier1,SRSF2|Tier1,CANT1|Tier1,YWHAE|Tier1,USP6|Tier1,PER1|Tier1,FLCN|Tier1,TAF15|Tier1,MLLT6|Tier1,LASP1|Tier1,CDK12|Tier1,RARA|Tier1,ETV4|Tier1,SPOP|Tier1,RNF43|Tier1,PPM1D|Tier1,CD79B|Tier1,DDX5|Tier1,PRKAR1A|Tier1,ASPSCR1|Tier1,RABEP1|Tier1,GAS7|Tier1,MAP2K4|Tier1,NCOR1|Tier1,SPECC1|Tier2,NF1|Tier1,SUZ12|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=DOC2B;DisruptR=	no	chr17p13.3-q25.3
chr18	10010	9868588	DEL	-0.654918484576942	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr18p11.32-p11.22
chr18	9868589	80263172	NEU	-0.119695815751723	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;COSMIC;Cancer_census=SMAD2|Tier1,SMAD4|Tier1,KDSR|Tier1,SS18|Tier1,SETBP1|Tier1,BCL2|Tier1,DCC|Tier2,ZNF521|Tier1,MALT1|Tier1;DisruptL=;DisruptR=	no	chr18p11.22-q23
chr19	90733	58607515	NEU	-0.0527598622410667	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;Cancer_census=FSTL3|Tier1,CD209|Tier2,KEAP1|Tier1,LYL1|Tier1,CEBPA|Tier1,BCL3|Tier1,BCL2L12|Tier2,KLK2|Tier1,TFPT|Tier2,STK11|Tier1,TCF3|Tier1,GNA11|Tier1,MAP2K2|Tier1,SH3GL1|Tier1,MLLT1|Tier1,MUC16|Tier2,CALR|Tier1,PRKACA|Tier1,DNAJB1|Tier1,BRD4|Tier1,TPM4|Tier1,JAK3|Tier1,ZNF429|Tier2,CCNE1|Tier1,CD79A|Tier1,CIC|Tier1,CBLC|Tier1,ERCC2|Tier1,BAX|Tier1,POLD1|Tier1,PPP2R1A|Tier1,ZNF331|Tier1,CNOT3|Tier1,VAV1|Tier2,DNM2|Tier1,SMARCA4|Tier1,ELL|Tier1,CRTC1|Tier1,CEP89|Tier2,LSM14A|Tier2,AKT2|Tier1;DisruptL=;DisruptR=	no	chr19p13.3-q13.43
chr20	67260	64334067	DUP	0.347095917187199	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_40	known=;Cancer_census=MAFB|Tier1,SIRPA|Tier2,SRC|Tier1,TOP1|Tier1,SDC4|Tier1,SALL4|Tier1,GNAS|Tier1,SS18L1|Tier1,PTK6|Tier1,CRNKL1|Tier2,ASXL1|Tier1,PLCG1|Tier1,NFATC2|Tier1,PTPRT|Tier1;DisruptL=;DisruptR=	no	chr20p13-q13.33
chr21	13044018	46699872	NEU	-0.0805622643719076	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_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	DUP	0.361066086318312	bicseq2	COLO-829-NovaSeq_80--COLO-829BL-NovaSeq_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