Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
view test-data/example.vcf @ 88:aaf98cdc5916 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
| author | yhoogstrate |
|---|---|
| date | Thu, 05 Nov 2015 06:09:01 -0500 |
| parents | |
| 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=41;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:236:41:41:0:41:100%:2.3541E-24:0:84:0:0:22:19 chr1 84 . G A . PASS ADP=59;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:59:59:0:59:100%:4.1056E-35:0:83:0:0:33:26 chr1 146 . T C . PASS ADP=81;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:81:81:0:81:100%:2.7329E-48:0:86:0:0:49:32 chr1 206 . A G . PASS ADP=79;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:79:79:0:79:100%:4.3185E-47:0:86:0:0:48:31 chr1 495 . T G . PASS ADP=65;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:65:65:0:65:100%:1.0519E-38:0:89:0:0:31:34 chr1 496 . A C . PASS ADP=64;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:64:64:0:64:100%:4.1752E-38:0:89:0:0:31:33 chr1 497 . G C . PASS ADP=63;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:63:63:0:63:100%:1.657E-37:0:89:0:0:30:33