Mercurial > repos > greg > cfsan_snp_pipeline_call_consensus_snps
diff test-data/input_snp_sites.vcf @ 0:3275d4866650 draft
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| author | greg |
|---|---|
| date | Fri, 13 Oct 2023 17:57:44 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_snp_sites.vcf Fri Oct 13 17:57:44 2023 +0000 @@ -0,0 +1,69 @@ +##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 +gi|9626243|ref|NC_001416.1| 2599 . C A . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:25:24:0:24:100%:3.101E-14:0:26:0:0:8:16 +gi|9626243|ref|NC_001416.1| 3678 . C 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 1/1:75:19:16:1:15:93.75%:2.8282E-8:17:26:1:0:8:7 +gi|9626243|ref|NC_001416.1| 5142 . C G . 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-10:0:27:0:0:4:13 +gi|9626243|ref|NC_001416.1| 5336 . G T . PASS ADP=8;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:41:8:8:0:8:100%:7.77E-5:0:31:0:0:1:7 +gi|9626243|ref|NC_001416.1| 5994 . 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 1/1:117:21:21:0:21:100%:1.8578E-12:0:24:0:0:10:11 +gi|9626243|ref|NC_001416.1| 6535 . C A . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:22:19:0:18:100%:1.1019E-10:0:27:0:0:6:12 +gi|9626243|ref|NC_001416.1| 7424 . G 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 1/1:117:25:21:0:21:100%:1.8578E-12:0:26:0:0:13:8 +gi|9626243|ref|NC_001416.1| 10127 . 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 1/1:146:32:26:0:26:100%:2.0165E-15:0:26:0:0:14:12 +gi|9626243|ref|NC_001416.1| 11782 . A G . 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 1/1:87:17:16:0:16:100%:1.6637E-9:0:28:0:0:7:9 +gi|9626243|ref|NC_001416.1| 13264 . C T . 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 1/1:123:23:22:0:22:100%:4.7526E-13:0:26:0:0:14:8 +gi|9626243|ref|NC_001416.1| 13542 . C G . 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 1/1:123:26:23:0:22:95.65%:4.7526E-13:0:29:0:0:14:8 +gi|9626243|ref|NC_001416.1| 13952 . G C . PASS ADP=31;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:176:33:31:0:31:100%:2.1486E-18:0:26:0:0:13:18 +gi|9626243|ref|NC_001416.1| 15715 . G C . 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 1/1:117:24:21:0:21:100%:1.8578E-12:0:28:0:0:15:6 +gi|9626243|ref|NC_001416.1| 15967 . A T . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:28:24:0:23:100%:1.2146E-13:0:24:0:0:13:10 +gi|9626243|ref|NC_001416.1| 17142 . G A . 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 1/1:129:27:23:0:23:100%:1.2146E-13:0:29:0:0:12:11 +gi|9626243|ref|NC_001416.1| 17311 . G C . PASS ADP=33;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:188:35:33:0:33:100%:1.3852E-19:0:26:0:0:14:19 +gi|9626243|ref|NC_001416.1| 17854 . G T . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:105:20:19:0:19:100%:2.8292E-11:0:26:0:0:5:14 +gi|9626243|ref|NC_001416.1| 18420 . G T . 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-10:0:26:0:0:9:8 +gi|9626243|ref|NC_001416.1| 18652 . G T . 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 1/1:129:25:23:0:23:100%:1.2146E-13:0:25:0:0:13:10 +gi|9626243|ref|NC_001416.1| 19208 . 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 1/1:87:17:16:0:16:100%:1.6637E-9:0:26:0:0:8:8 +gi|9626243|ref|NC_001416.1| 20367 . G C . PASS ADP=30;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:170:32:30:0:30:100%:8.4556E-18:0:27:0:0:19:11 +gi|9626243|ref|NC_001416.1| 21320 . T 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 1/1:129:25:23:0:23:100%:1.2146E-13:0:29:0:0:11:12 +gi|9626243|ref|NC_001416.1| 22220 . A C . PASS ADP=27;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:152:28:27:0:27:100%:5.1363E-16:0:23:0:0:17:10 +gi|9626243|ref|NC_001416.1| 22747 . G A . 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 1/1:99:19:18:0:18:100%:1.1019E-10:0:28:0:0:6:12 +gi|9626243|ref|NC_001416.1| 23457 . A C . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:20:19:0:18:100%:1.1019E-10:0:27:0:0:11:7 +gi|9626243|ref|NC_001416.1| 25005 . 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 1/1:58:12:11:0:11:100%:1.4176E-6:0:26:0:0:5:6 +gi|9626243|ref|NC_001416.1| 25158 . A C . 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-12:0:27:0:0:10:10 +gi|9626243|ref|NC_001416.1| 25645 . C G . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:26:24:0:24:100%:3.101E-14:0:26:0:0:10:14 +gi|9626243|ref|NC_001416.1| 26173 . G C . 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 1/1:117:21:21:0:21:100%:1.8578E-12:0:26:0:0:10:11 +gi|9626243|ref|NC_001416.1| 27661 . T 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 1/1:123:25:23:0:22:100%:4.7526E-13:0:28:0:0:14:8 +gi|9626243|ref|NC_001416.1| 28045 . G T . 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 1/1:141:25:25:0:25:100%:7.9107E-15:0:29:0:0:13:12 +gi|9626243|ref|NC_001416.1| 28362 . T C . 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-12:0:24:0:0:12:8 +gi|9626243|ref|NC_001416.1| 29411 . T C . PASS ADP=28;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:158:31:28:0:28:100%:1.3074E-16:0:28:0:0:13:15 +gi|9626243|ref|NC_001416.1| 30125 . A G . 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 1/1:117:21:21:0:21:100%:1.8578E-12:0:29:0:0:11:10 +gi|9626243|ref|NC_001416.1| 34137 . T G . PASS ADP=33;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:182:34:33:0:32:100%:5.4567E-19:0:25:0:0:17:15 +gi|9626243|ref|NC_001416.1| 35907 . G T . PASS ADP=31;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:164:32:31:0:29:100%:3.3259E-17:0:27:0:0:18:11 +gi|9626243|ref|NC_001416.1| 38575 . A C . 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 1/1:117:21:21:0:21:100%:1.8578E-12:0:28:0:0:10:11 +gi|9626243|ref|NC_001416.1| 39206 . T 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-10:0:24:0:0:7:10 +gi|9626243|ref|NC_001416.1| 39484 . C A . 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 1/1:99:20:18:0:18:100%:1.1019E-10:0:24:0:0:11:7 +gi|9626243|ref|NC_001416.1| 43470 . G 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 1/1:117:25:21:0:21:100%:1.8578E-12:0:29:0:0:12:9 +gi|9626243|ref|NC_001416.1| 44134 . T C . 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 1/1:111:22:21:0:20:100%:7.2544E-12:0:25:0:0:12:8 +gi|9626243|ref|NC_001416.1| 44413 . G T . PASS ADP=31;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:176:32:31:0:31:100%:2.1486E-18:0:26:0:0:13:18 +gi|9626243|ref|NC_001416.1| 45364 . A C . PASS ADP=27;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:141:27:27:0:25:96.15%:7.9107E-15:0:27:0:0:16:9 +gi|9626243|ref|NC_001416.1| 47425 . T 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 1/1:93:19:18:0:17:100%:4.2852E-10:0:26:0:0:11:6 +