Mercurial > repos > jpayne > snp_pipeline

comparison test-data/snpma.vcf @ 58:d53281e6edae

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author jpayne
date Mon, 17 Jun 2024 02:57:10 -0400
parents eefdd97a6749
children
comparison
equal deleted inserted replaced
57:d3095ad12f24 58:d53281e6edae
17 ##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60"> 17 ##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60">
18 ##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand"> 18 ##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand">
19 ##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand"> 19 ##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand">
20 ##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig."> 20 ##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig.">
21 ##contig=<ID=gi|9626243|ref|NC_001416.1|> 21 ##contig=<ID=gi|9626243|ref|NC_001416.1|>
22 ##bcftools_mergeVersion=1.3.1+htslib-1.3.1 22 ##bcftools_mergeVersion=1.9+htslib-1.9
23 ##bcftools_mergeCommand=merge -o ./snpma.vcf --merge all --info-rules NS:sum ./tmp.vcf.PYaZFQ/sample1.vcf.gz ./tmp.vcf.PYaZFQ/sample2.vcf.gz ./tmp.vcf.PYaZFQ/sample3.vcf.gz ./tmp.vcf.PYaZFQ/sample4.vcf.gz 23 ##bcftools_mergeCommand=merge -o snpma.vcf --merge all --info-rules NS:sum tmp.vcf.3imm9gjk/sample1.vcf.gz tmp.vcf.3imm9gjk/sample2.vcf.gz tmp.vcf.3imm9gjk/sample3.vcf.gz tmp.vcf.3imm9gjk/sample4.vcf.gz; Date=Mon Aug 1 12:20:35 2022
24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4 24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4
25 gi|9626243|ref|NC_001416.1| 403 . G A . PASS NS=4 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:13:14:PASS 0:24:24:0:11:13:0:0:PASS 0:26:26:0:13:13:0:0:PASS 0:15:15:0:11:4:0:0:PASS 25 gi|9626243|ref|NC_001416.1| 403 . G A . PASS NS=4 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:13:14:PASS 0:24:24:0:11:13:0:0:PASS 0:26:26:0:13:13:0:0:PASS 0:15:15:0:11:4:0:0:PASS
26 gi|9626243|ref|NC_001416.1| 550 . G A . PASS NS=4 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:21:1:13:8:0:1:PASS 0:26:26:0:14:12:0:0:PASS 0:29:29:0:13:16:0:0:PASS 1:26:0:26:0:0:14:12:PASS 26 gi|9626243|ref|NC_001416.1| 550 . G A . PASS NS=4 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:21:1:13:8:0:1:PASS 0:26:26:0:14:12:0:0:PASS 0:29:29:0:13:16:0:0:PASS 1:26:0:26:0:0:14:12:PASS
27 gi|9626243|ref|NC_001416.1| 586 . C G . PASS NS=4 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:12:6:0:0:PASS 0:23:23:0:12:11:0:0:PASS 0:37:37:0:15:22:0:0:PASS 1:27:0:25:0:0:17:8:PASS 27 gi|9626243|ref|NC_001416.1| 586 . C G . PASS NS=4 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:12:6:0:0:PASS 0:23:23:0:12:11:0:0:PASS 0:37:37:0:15:22:0:0:PASS 1:27:0:25:0:0:17:8:PASS
28 gi|9626243|ref|NC_001416.1| 753 . G A . PASS NS=4 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:24:0:0:16:8:PASS 0:27:27:0:10:17:0:0:PASS 0:26:24:2:13:11:0:2:PASS 0:23:23:0:12:11:0:0:PASS 28 gi|9626243|ref|NC_001416.1| 753 . G A . PASS NS=4 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:24:0:0:16:8:PASS 0:27:27:0:10:17:0:0:PASS 0:26:24:2:13:11:0:2:PASS 0:23:23:0:12:11:0:0:PASS