Mercurial > repos > iuc > varscan_mpileup

annotate test-data/varscan_somatic_snp_result1.vcf @ 1:0bc800d67a0e 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 09:19:37 -0400
parents 1e667badbe87
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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1 ##fileformat=VCFv4.1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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2 ##source=VarScan2
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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4 ##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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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)">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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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">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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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">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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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">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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9 ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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10 ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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11 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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12 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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13 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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14 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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15 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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16 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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17 ##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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18 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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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
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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22 chr1 51439628 . T C . str10 DP=237;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.8101E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:123:123:0:0%:77,46,0,0 0/1:.:114:113:1:0.88%:74,39,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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23 chr1 51439638 . G A . str10 DP=234;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.9145E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:119:119:0:0%:72,47,0,0 0/1:.:115:114:1:0.87%:75,39,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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24 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
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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25 chr1 51439671 . G A . str10 DP=222;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.045E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:110:110:0:0%:53,57,0,0 0/1:.:112:111:1:0.89%:59,52,1,0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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26 chr1 51439684 . G T . str10 DP=210;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.9524E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:106:106:0:0%:51,55,0,0 0/1:.:104:103:1:0.96%:53,50,1,0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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27 chr1 51439703 . C T . str10 DP=202;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.099E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:99:99:0:0%:46,53,0,0 0/1:.:103:102:1:0.97%:48,54,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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28 chr1 51439705 . G T . str10 DP=204;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1961E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:98:98:0:0%:42,56,0,0 0/1:.:106:105:1:0.94%:48,57,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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29 chr1 51439706 . G T . str10 DP=201;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1741E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:97:97:0:0%:41,56,0,0 0/1:.:104:103:1:0.96%:46,57,1,0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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30 chr1 51439726 . C G . str10 DP=187;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1872E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:90:90:0:0%:37,53,0,0 0/1:.:97:96:1:1.03%:44,52,1,0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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31 chr1 51439751 . C G . str10 DP=168;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.3293E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:79:78:0:0%:28,50,0,0 0/1:.:89:88:1:1.12%:35,53,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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32 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
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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33 chr1 51439766 . G T . str10 DP=154;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1299E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:75:75:0:0%:34,41,0,0 0/1:.:79:78:1:1.27%:30,48,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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34 chr1 51439788 . T C . str10 DP=136;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1471E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:66:66:0:0%:21,45,0,0 0/1:.:70:69:1:1.43%:24,45,1,0
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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35 chr1 51439828 . G A . str10 DP=122;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.7377E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:52:52:0:0%:14,38,0,0 0/1:.:70:69:1:1.43%:27,42,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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36 chr1 51439832 . C G . str10 DP=125;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.52E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:56:56:0:0%:14,42,0,0 0/1:.:69:68:1:1.45%:25,43,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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37 chr1 51439876 . T G . str10 DP=105;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.619E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:46:46:0:0%:10,36,0,0 0/1:.:59:58:1:1.69%:23,35,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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38 chr1 51439882 . G T . str10 DP=105;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.2381E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:13,37,0,0 0/1:.:55:54:1:1.82%:22,32,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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39 chr1 51439889 . G T . str10 DP=97;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1546E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:47:47:0:0%:14,33,0,0 0/1:.:50:49:1:2%:21,28,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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40 chr1 51439953 . G T . str10 DP=59;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.9322E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:24:24:0:0%:5,19,0,0 0/1:.:35:34:1:2.86%:7,27,0,1
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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41 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