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annotate test-data/varscan_somatic_snp_result2.vcf @ 1:8d8de66233ea draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
author iuc
date Sun, 15 Jul 2018 09:19:48 -0400
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8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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1 ##fileformat=VCFv4.1
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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2 ##source=VarScan2
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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4 ##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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5 ##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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6 ##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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7 ##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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8 ##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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9 ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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10 ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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11 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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12 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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13 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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14 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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15 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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16 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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17 ##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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18 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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19 chr1 51436072 . C A . PASS DP=47;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.4681E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:26:26:0:0%:23,3,0,0 0/1:.:21:20:1:4.76%:19,1,1,0
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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20 chr1 51436311 . T C . PASS DP=16;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.375E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:9:9:0:0%:1,8,0,0 0/1:.:7:6:1:14.29%:0,6,0,1
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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21 chr1 51436320 . G A . PASS DP=19;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.2632E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:9:9:0:0%:1,8,0,0 0/1:.:10:9:1:10%:0,9,0,1
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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22 chr1 51439665 . C T . PASS DP=226;SOMATIC;SS=2;SSC=9;GPV=1E0;SPV=1.2006E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:114:114:0:0%:56,58,0,0 0/1:.:112:109:3:2.68%:63,46,2,1
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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23 chr1 51439763 . G A . PASS DP=159;SOMATIC;SS=2;SSC=5;GPV=1E0;SPV=2.7092E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:76:76:0:0%:34,42,0,0 0/1:.:83:81:2:2.41%:32,49,1,1
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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24 chr1 51440025 . A C . PASS DP=27;SOMATIC;SS=2;SSC=1;GPV=1E0;SPV=6.6667E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:9:9:0:0%:1,8,0,0 0/1:.:18:17:1:5.56%:1,16,0,1
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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25 chr1 51440035 . G T . PASS DP=21;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=6.1905E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:8:8:0:0%:1,7,0,0 0/1:.:13:12:1:7.69%:1,11,0,1
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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26 chr1 51440056 . T G . PASS DP=22;SOMATIC;SS=2;SSC=1;GPV=1E0;SPV=6.3636E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:8:8:0:0%:1,7,0,0 0/1:.:14:13:1:7.14%:1,12,0,1