Mercurial > repos > jpayne > snp_pipeline
view test-data/samples/sample4/var.flt_removed.vcf @ 58:d53281e6edae
planemo upload
| author | jpayne |
|---|---|
| date | Mon, 17 Jun 2024 02:57:10 -0400 |
| parents | eefdd97a6749 |
| 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"> ##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)"> ##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"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 gi|9626243|ref|NC_001416.1| 1019 . C T . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:22:20:0:20:100%:7.2544E-12:0:25:0:0:7:13 gi|9626243|ref|NC_001416.1| 1620 . G A . PASS ADP=17;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:19:17:0:17:100%:4.2852E-10:0:26:0:0:7:10 gi|9626243|ref|NC_001416.1| 1650 . G C . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:141:26:25:0:25:100%:7.9107E-15:0:26:0:0:10:15 gi|9626243|ref|NC_001416.1| 1788 . A T . PASS ADP=16;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:87:16:16:0:16:100%:1.6637E-9:0:26:0:0:9:7 gi|9626243|ref|NC_001416.1| 2452 . A T . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:103:23:21:1:20:95.24%:4.0873E-11:33:27:1:0:13:7 gi|9626243|ref|NC_001416.1| 26972 . A T . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:103:22:21:1:20:95.24%:4.0873E-11:35:26:1:0:11:9 gi|9626243|ref|NC_001416.1| 27539 . A C . PASS ADP=11;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:58:11:11:0:11:100%:1.4176E-6:0:30:0:0:5:6 gi|9626243|ref|NC_001416.1| 27722 . C A . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:141:26:25:0:25:100%:7.9107E-15:0:24:0:0:15:10 gi|9626243|ref|NC_001416.1| 27825 . A G . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:22:20:0:20:100%:7.2544E-12:0:27:0:0:13:7