Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
view test-data/example.vcf @ 1:9a39c4105901 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
author | erasmus-medical-center |
---|---|
date | Wed, 15 Feb 2017 16:16:01 -0500 |
parents | 0c5cc5763091 |
children |
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##fileformat=VCFv4.1 ##source=VarScan2 ##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15"> ##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)"> ##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant"> ##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant"> ##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called"> ##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=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15"> ##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=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test"> ##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)"> ##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)"> ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)"> ##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)"> ##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)"> ##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 chr1 24 . C G . PASS ADP=50;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:50:50:0:50:100%:9.9117E-30:0:93:0:0:27:23 chr1 84 . G A . PASS ADP=70;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:70:70:0:70:100%:1.0659E-41:0:93:0:0:38:32 chr1 146 . T C . PASS ADP=85;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:85:85:0:85:100%:1.0935E-50:0:93:0:0:52:33 chr1 206 . A G . PASS ADP=91;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:91:91:0:91:100%:2.7621E-54:0:93:0:0:51:40 chr1 495 . T G . PASS ADP=75;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:75:75:0:75:100%:1.0773E-44:0:93:0:0:37:38 chr1 496 . A C . PASS ADP=76;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:76:76:0:76:100%:2.711E-45:0:93:0:0:38:38 chr1 497 . G C . PASS ADP=77;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:77:77:0:77:100%:6.8219E-46:0:93:0:0:38:39