Mercurial > repos > jpayne > snp_pipeline

annotate test-data/samples/sample1/var.flt_removed.vcf @ 58:d53281e6edae

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planemo upload
author jpayne
date Mon, 17 Jun 2024 02:57:10 -0400
parents eefdd97a6749
children
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jpayne@0 1 ##fileformat=VCFv4.1
jpayne@0 2 ##source=VarScan2
jpayne@0 3 ##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
jpayne@0 4 ##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
jpayne@0 5 ##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
jpayne@0 6 ##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
jpayne@0 7 ##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
jpayne@0 8 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
jpayne@0 9 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
jpayne@0 10 ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
jpayne@0 11 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
jpayne@0 12 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
jpayne@0 13 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
jpayne@0 14 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
jpayne@0 15 ##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
jpayne@0 16 ##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
jpayne@0 17 ##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
jpayne@0 18 ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
jpayne@0 19 ##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
jpayne@0 20 ##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
jpayne@0 21 ##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
jpayne@0 22 ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
jpayne@0 23 ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
jpayne@0 24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
jpayne@0 25 gi|9626243|ref|NC_001416.1| 403 . G A . PASS ADP=26;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:146:27:26:0:26:100%:2.0165E-15:0:31:0:0:12:14
jpayne@0 26 gi|9626243|ref|NC_001416.1| 1079 . T 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 1/1:135:26:25:0:24:100%:3.101E-14:0:26:0:0:9:15
jpayne@0 27 gi|9626243|ref|NC_001416.1| 1540 . A G . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:24:22:0:22:100%:4.7526E-13:0:24:0:0:13:9
jpayne@0 28 gi|9626243|ref|NC_001416.1| 1804 . G C . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:23:23:0:23:100%:1.2146E-13:0:28:0:0:11:12
jpayne@0 29 gi|9626243|ref|NC_001416.1| 2123 . G C . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:24:23:0:23:100%:1.2146E-13:0:27:0:0:10:13
jpayne@0 30 gi|9626243|ref|NC_001416.1| 4977 . G A . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:25:22:0:22:100%:4.7526E-13:0:27:0:0:10:12
jpayne@0 31 gi|9626243|ref|NC_001416.1| 5482 . 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 1/1:93:18:17:0:17:100%:4.2852E-10:0:28:0:0:8:9
jpayne@0 32 gi|9626243|ref|NC_001416.1| 5516 . T A . PASS ADP=13;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:70:16:13:0:13:100%:9.6148E-8:0:23:0:0:7:6
jpayne@0 33 gi|9626243|ref|NC_001416.1| 5800 . G A . PASS ADP=13;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:70:19:13:0:13:100%:9.6148E-8:0:26:0:0:4:9
jpayne@0 34 gi|9626243|ref|NC_001416.1| 27790 . A C . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:20:18:0:17:100%:4.2852E-10:0:26:0:0:6:11
jpayne@0 35 gi|9626243|ref|NC_001416.1| 34370 . A G . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:23:22:0:21:100%:1.8578E-12:0:26:0:0:10:11
jpayne@0 36 gi|9626243|ref|NC_001416.1| 34812 . A C . 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 1/1:81:16:16:0:15:100%:6.4467E-9:0:26:0:0:11:4
jpayne@0 37 gi|9626243|ref|NC_001416.1| 34920 . T C . PASS ADP=15;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:81:16:15:0:15:100%:6.4467E-9:0:23:0:0:9:6
jpayne@0 38 gi|9626243|ref|NC_001416.1| 35148 . C A . 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-9:0:26:0:0:10:6