Mercurial > repos > elixir-it > somaticsniper

annotate test-data/sniper_results.vcf @ 2:f7d69881bdec draft default tip

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author elixir-it
date Sat, 21 Sep 2019 13:22:28 -0400
parents 70999d19997f
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1 ##fileformat=VCFv4.1
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2 ##fileDate=20180622
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3 ##phasing=none
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4 ##reference=file:///export/gatkhg38pl/GRCh38.d1.vd1.fa
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5 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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6 ##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
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7 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
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8 ##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
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elixir-it
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9 ##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
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10 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
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11 ##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
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12 ##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
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13 ##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality">
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14 ##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality across all reads">
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15 ##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
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16 ##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown">
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17 ##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score">
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18 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
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19 chr22 22714396 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:15:0,15,0,0:0,0,15,0:72:.:0:30:60:60:0:. 0/1:0/1:41:0,28,0,13:13,0,28,0:59:.:59:30,31:60:60,60:2:45
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20 chr22 22714411 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:0,9,0,0:0,0,0,9:54:.:0:30:60:60:0:. 0/1:0/1:28:0,22,0,6:0,6,0,22:32:.:32:32,31:60:60,60:2:27