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view test-data/varscan_somatic_snp_result1.vcf @ 0:1e667badbe87 draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
author iuc
date Tue, 10 Jul 2018 13:36:03 -0400
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##fileformat=VCFv4.1
##source=VarScan2
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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