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test.vcf
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test.vcf
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##fileformat=VCFv4.2
##fileDate=20160216
##source=snowman run -t /xchip/gistic/Jeremiah/Data/HCC1143_mem.bam -n /xchip/gistic/Jeremiah/Data/HCC1143_BL_mem.bam -a full -p 15 -D /xchip/gistic/Jeremiah/Projects/SnowmanFilters/dbsnp_138.b37_indel.vcf
##reference=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=X,length=155270560>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=20,length=63025520>
##contig=<ID=Y,length=59373566>
##contig=<ID=19,length=59128983>
##contig=<ID=22,length=51304566>
##contig=<ID=21,length=48129895>
##contig=<ID=GL000192.1,length=547496>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000222.1,length=186861>
##contig=<ID=GL000212.1,length=186858>
##contig=<ID=GL000195.1,length=182896>
##contig=<ID=GL000223.1,length=180455>
##contig=<ID=GL000224.1,length=179693>
##contig=<ID=GL000219.1,length=179198>
##contig=<ID=GL000205.1,length=174588>
##contig=<ID=GL000215.1,length=172545>
##contig=<ID=GL000216.1,length=172294>
##contig=<ID=GL000217.1,length=172149>
##contig=<ID=NC_007605,length=171823>
##contig=<ID=GL000199.1,length=169874>
##contig=<ID=GL000211.1,length=166566>
##contig=<ID=GL000213.1,length=164239>
##contig=<ID=GL000220.1,length=161802>
##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000209.1,length=159169>
##contig=<ID=GL000221.1,length=155397>
##contig=<ID=GL000214.1,length=137718>
##contig=<ID=GL000228.1,length=129120>
##contig=<ID=GL000227.1,length=128374>
##contig=<ID=GL000191.1,length=106433>
##contig=<ID=GL000208.1,length=92689>
##contig=<ID=GL000198.1,length=90085>
##contig=<ID=GL000204.1,length=81310>
##contig=<ID=GL000233.1,length=45941>
##contig=<ID=GL000237.1,length=45867>
##contig=<ID=GL000230.1,length=43691>
##contig=<ID=GL000242.1,length=43523>
##contig=<ID=GL000243.1,length=43341>
##contig=<ID=GL000241.1,length=42152>
##contig=<ID=GL000236.1,length=41934>
##contig=<ID=GL000240.1,length=41933>
##contig=<ID=GL000206.1,length=41001>
##contig=<ID=GL000232.1,length=40652>
##contig=<ID=GL000234.1,length=40531>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000244.1,length=39929>
##contig=<ID=GL000248.1,length=39786>
##contig=<ID=GL000196.1,length=38914>
##contig=<ID=GL000249.1,length=38502>
##contig=<ID=GL000246.1,length=38154>
##contig=<ID=GL000203.1,length=37498>
##contig=<ID=GL000197.1,length=37175>
##contig=<ID=GL000245.1,length=36651>
##contig=<ID=GL000247.1,length=36422>
##contig=<ID=GL000201.1,length=36148>
##contig=<ID=GL000235.1,length=34474>
##contig=<ID=GL000239.1,length=33824>
##contig=<ID=GL000210.1,length=27682>
##contig=<ID=GL000231.1,length=27386>
##contig=<ID=GL000229.1,length=19913>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000226.1,length=15008>
##contig=<ID=GL000207.1,length=4262>
##INFO=<ID=LOD,Number=1,Type=Float,Description="Log of the odds that variant is real vs artifact">
##INFO=<ID=READNAMES,Number=.,Type=String,Description="IDs of ALT reads">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Variant is somatic">
##INFO=<ID=GRAYLIST,Number=0,Type=Flag,Description="Indel is low quality and cross a difficult region of genome">
##INFO=<ID=REPSEQ,Number=1,Type=String,Description="Repeat sequence near the event">
##INFO=<ID=SPAN,Number=1,Type=Integer,Description="Size of the indel">
##INFO=<ID=NM,Number=1,Type=Integer,Description="Number of mismatches of this alignment fragment to reference">
##INFO=<ID=PON,Number=1,Type=Integer,Description="Number of normal samples that have this indel present">
##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Mapping quality (BWA-MEM) of the assembled contig">
##INFO=<ID=SCTG,Number=1,Type=String,Description="Identifier for the contig assembled by SnowmanSV to make the indel call">
##FILTER=<ID=LOWNORMCOV,Description="Fewer than 5 normal reads at this site">
##FILTER=<ID=GRAYLISTANDPON,Description="Indel overlaps with panel of normals, and has overlap with tricky genomic region">
##FILTER=<ID=PASS,Description="3+ split reads, 60 contig MAPQ">
##FILTER=<ID=LOWAF,Description="LOD score < cutoff with --lod or allelic fraction < 0.05">
##FILTER=<ID=WEAKCIGARMATCH,Description="For indels <= 5 bp, require 8+ split reads or 4+ and 3+ cigar matches">
##FILTER=<ID=WEAKASSEMBLY,Description="4 or fewer split reads">
##FILTER=<ID=GERMLOWAF,Description="Germline variant with support for being AF of 0.5+ (LR) less than cutoff">
##FILTER=<ID=LOWMAPQ,Description="Assembly contig has less than MAPQ 10">
##FORMAT=<ID=SL,Number=1,Type=Float,Description="Alignment-quality Scaled log-odds, where LO is LO * (MAPQ - 2*NM)/60">
##FORMAT=<ID=LR,Number=1,Type=Float,Description="Log-odds that this variant is AF=0 vs AF>=0.5">
##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of spanning reads for this variants">
##FORMAT=<ID=PL,Number=1,Type=Integer,Description="Normalized likelihood of the current genotype (currently not supported, always 0)">
##FORMAT=<ID=GQ,Number=1,Type=String,Description="Genotype quality (currently not supported. Always 0)">
##FORMAT=<ID=LO,Number=1,Type=Float,Description="Log-odds that this variant is real vs artifact">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth of coverage: Number of reads covering site.">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele depth: Number of reads supporting the variant">
##FORMAT=<ID=CR,Number=1,Type=Integer,Description="Number of cigar-supported reads for this variant">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype (currently not supported. Always 0/1)">
##SAMPLE=<ID=/xchip/gistic/Jeremiah/Data/HCC1143_mem.bam>
##SAMPLE=<ID=/xchip/gistic/Jeremiah/Data/HCC1143_BL_mem.bam>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /xchip/gistic/Jeremiah/Data/HCC1143_BL_mem.bam /xchip/gistic/Jeremiah/Data/HCC1143_mem.bam
1 4099803 5093 T TGTG 99 PASS LOD=14.38;MAPQ=60;NM=6;READNAMES=x;REPSEQ=AAAAAAAAAA;SCTG=c_1_4091501_4116501_1728C;SOMATIC;SPAN=3 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:66:0:0:0:0:19.87:0:0 0/1:15:70:0:0:9:15:-8.928:14.38:11.5
1 11439833 12916 AC A 99 PASS LOD=116.1;MAPQ=60;NM=0;READNAMES=x;REPSEQ=AAA;SCTG=c_1_11417001_11442001_1156C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:124:0:0:0:0:37.33:0:0 0/1:37:118:0:0:17:37:-112.5:116.1:116.1
1 14942339 15565 CATTTCTGA C 99 PASS LOD=85.16;MAPQ=60;NM=0;READNAMES=x;REPSEQ=CC;SCTG=c_1_14920501_14945501_1351C;SOMATIC;SPAN=8 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:120:0:0:0:0:36.12:0:0 0/1:28:108:0:0:26:28:-79.49:85.16:85.16
1 15682315 16005 CTCCCAGGCAAG C 99 PASS LOD=82.81;MAPQ=60;NM=2;READNAMES=x;REPSEQ=AA;SCTG=c_1_15680001_15705001_1508C;SOMATIC;SPAN=11 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:121:0:0:0:0:36.42:0:0 0/1:27:99:0:0:26:27:-78.2:82.81:77.29
1 38902271 35676 TA T 99 PASS LOD=15.75;MAPQ=60;NM=1;READNAMES=x;REPSEQ=AAAAAAAA;SCTG=c_1_38881501_38906501_937C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:32:0:0:0:0:9.633:0:0 0/1:8:20:0:0:6:8:-15.57:15.75:15.22
1 39525575 36160 T TA 99 PASS LOD=14.33;MAPQ=60;NM=0;READNAMES=x;REPSEQ=AAAAAAAAAAA;SCTG=c_1_39518501_39543501_1148C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:1:87:0:0:1:0:24.79:-0.3299:-0.3299 0/1:25:77:0:0:23:25:-11.77:14.33:14.33
1 48468636 44071 CT C 99 PASS LOD=20.56;MAPQ=60;NM=1;READNAMES=x;REPSEQ=TTTTTTTTT;SCTG=c_1_48461001_48486001_214C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:1:40:0:0:1:1:9.518:0.5389:0.5209 0/1:14:66:0:0:11:14:-15.45:20.56:19.87
1 48815931 44181 AT A 99 PASS DBSNP=TRUE;LOD=24.75;MAPQ=60;NM=0;READNAMES=x;REPSEQ=TTTTTTTTTT;SCTG=c_1_48804001_48829001_365C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:66:0:0:0:0:19.87:0:0 0/1:23:84:0:0:10:23:-20.71:24.75:24.75
1 51821226 46045 G GT 99 PASS DBSNP=TRUE;LOD=77.19;MAPQ=60;NM=1;READNAMES=x;REPSEQ=TTTTTTTT;SCTG=c_1_51817501_51842501_1497C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:56:0:0:0:0:16.86:0:0 0/1:38:85:0:0:28:38:-76.97:77.19:74.62
1 52315493 46583 C CA 99 PASS LOD=42.12;MAPQ=60;NM=0;READNAMES=x;REPSEQ=AAAAAAAAAA;SCTG=c_1_52307501_52332501_1048C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:108:0:0:0:0:32.51:0:0 0/1:38:130:0:0:22:38:-36.87:42.12:42.12
1 70815825 59243 C CA 99 PASS LOD=38.84;MAPQ=60;NM=0;READNAMES=x;REPSEQ=AAAAAAA;SCTG=c_1_70805001_70830001_385C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:84:0:0:0:0:25.29:0:0 0/1:19:73:0:0:14:19:-35.02:38.84:38.84
1 72689198 60728 CT C 99 PASS LOD=30.29;MAPQ=60;NM=0;READNAMES=x;REPSEQ=TT;SCTG=c_1_72667001_72692001_694C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:81:0:0:0:0:24.38:0:0 0/1:11:77:0:0:11:11:-20.82:30.29:30.29
1 78512468 64714 GA G 99 PASS LOD=35.05;MAPQ=60;NM=1;READNAMES=x;REPSEQ=AAAAAAAAA;SCTG=c_1_78498001_78523001_575C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:125:0:0:0:0:37.63:0:0 0/1:24:115:0:0:12:24:-25.93:35.05:33.89
1 80023744 65624 TG T 99 PASS LOD=71.6;MAPQ=60;NM=1;READNAMES=x;REPSEQ=CC;SCTG=c_1_80017001_80042001_1057C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:89:0:0:0:0:26.79:0:0 0/1:24:104:0:0:20:24:-64.69:71.6:69.22
1 90549816 73294 GA G 99 PASS LOD=78.6;MAPQ=60;NM=0;READNAMES=x;REPSEQ=AA;SCTG=c_1_90527501_90552501_736C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:112:0:0:0:0:33.72:0:0 0/1:26:104:0:0:20:26:-72.69:78.6:78.6
1 102149804 81384 GTCTGACCAACGTTTGTAATAACATATCCATGAAAAAAAAATATCAAATT G 99 PASS LOD=46.91;MAPQ=60;NM=1;READNAMES=x;SCTG=c_1_102140501_102165501_731C;SOMATIC;SPAN=49 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:112:0:0:0:0:33.72:0:0 0/1:16:77:0:0:16:0:-40.82:46.91:45.35
1 105990617 83703 TG T 99 PASS LOD=81.94;MAPQ=60;NM=0;READNAMES=x;REPSEQ=AAAAA;SCTG=c_1_105987001_106012001_210C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:108:0:0:0:0:32.51:0:0 0/1:27:60:0:0:23:27:-81.81:81.94:81.94
1 109175699 85349 GC G 99 PASS LOD=72.08;MAPQ=60;NM=0;READNAMES=x;SCTG=c_1_109172001_109197001_307C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:91:0:0:0:0:27.39:0:0 0/1:23:74:0:0:16:23:-69.72:72.08:72.08
1 114428673 89982 TA T 99 PASS LOD=48.95;MAPQ=60;NM=0;READNAMES=x;REPSEQ=AAAAAA;SCTG=c_1_114415001_114440001_438C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:54:0:0:0:0:16.26:0:0 0/1:19:47:0:0:6:19:-48.57:48.95:48.95
1 114540407 90128 AT A 99 PASS DBSNP=TRUE;LOD=70.51;MAPQ=60;NM=1;READNAMES=x;REPSEQ=TTTTTTTT;SCTG=c_1_114537501_114562501_366C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:71:0:0:0:0:21.37:0:0 0/1:32:54:0:0:23:32:-70.51:70.51:68.16
1 118173006 92693 GCCA G 99 PASS LOD=99.78;MAPQ=60;NM=0;READNAMES=x;REPSEQ=CCC;SCTG=c_1_118163501_118188501_700C;SOMATIC;SPAN=3 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:127:0:0:0:0:38.23:0:0 0/1:31:85:0:0:28:31:-98.41:99.78:99.78
1 154669743 113124 G GT 99 PASS LOD=43.68;MAPQ=60;NM=0;READNAMES=x;REPSEQ=GGGGG;SCTG=c_1_154668501_154693501_1319C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:118:0:0:0:0:35.52:0:0 0/1:17:93:0:0:13:17:-34.89:43.68:43.68
1 159511118 116958 CA C 99 PASS LOD=84.44;MAPQ=60;NM=1;READNAMES=x;REPSEQ=AAA;SCTG=c_1_159495001_159520001_1269C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:100:0:0:0:0:30.1:0:0 0/1:27:88:0:0:19:27:-81.51:84.44:81.62
1 165840409 121508 TGC T 99 PASS LOD=9.597;MAPQ=60;NM=0;READNAMES=x;REPSEQ=GTGTGT;SCTG=c_1_165816001_165841001_1416C;SOMATIC;SPAN=2 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:128:0:0:0:0:38.53:0:0 0/1:6:115:0:0:3:6:14.81:9.597:9.597
1 170974122 125308 AT A 99 PASS DBSNP=TRUE;LOD=88.79;MAPQ=60;NM=0;READNAMES=x;REPSEQ=TTTTTTTTTT;SCTG=c_1_170961001_170986001_1029C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:1:91:0:0:1:1:25.39:-0.1145:-0.1145 0/1:60:105:0:0:37:60:-88.79:88.79:88.79
1 174182428 127789 TG T 99 PASS LOD=14.34;MAPQ=60;NM=0;READNAMES=x;REPSEQ=GG;SCTG=c_1_174170501_174195501_1198C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:108:0:0:0:0:32.51:0:0 0/1:6:93:0:0:6:6:3.996:14.34:14.34
1 176466739 128990 C CA 99 PASS LOD=22.2;MAPQ=60;NM=0;READNAMES=x;REPSEQ=AAAAAAAAA;SCTG=c_1_176449001_176474001_1047C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:68:0:0:0:0:20.47:0:0 0/1:15:69:0:0:15:14:-17.07:22.2:22.2
1 181761320 133129 GA G 99 PASS DBSNP=TRUE;LOD=236.6;MAPQ=60;NM=0;READNAMES=x;REPSEQ=AAAAAA;SCTG=c_1_181741001_181766001_1395C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:113:0:0:0:0:34.02:0:0 0/1:83:131:0:0:62:83:-236.6:236.6:236.6
1 184963190 135220 TA T 99 PASS LOD=9.293;MAPQ=60;NM=0;READNAMES=x;REPSEQ=TTTTTTTTTT;SCTG=c_1_184950501_184975501_1050C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:102:0:0:0:0:30.71:0:0 0/1:12:84:0:0:8:12:1.287:9.293:9.293
1 185540320 135702 GA G 99 PASS DBSNP=TRUE;LOD=58.5;MAPQ=60;NM=0;READNAMES=x;REPSEQ=AAAAAA;SCTG=c_1_185538501_185563501_562C;SOMATIC;SPAN=1 GT:AD:DP:GQ:PL:SR:CR:LR:LO:SL 0/1:0:131:0:0:0:0:39.43:0:0 0/1:25:97:0:0:21:25:-53.33:58.5:58.5