Mercurial > repos > dfornika > snippy

diff test-data/out/snps.subs.vcf @ 1:e7e5da92d0ab draft

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planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
author dfornika
date Fri, 18 Jan 2019 19:35:46 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out/snps.subs.vcf	Fri Jan 18 19:35:46 2019 -0500
@@ -0,0 +1,37 @@
+##fileformat=VCFv4.2
+##snippy="snippy-vcf_extract_subs snps.filt.vcf"
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190118
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=Wildtype,length=197394>
+##phasing=none
+##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Wildtype:0-13379"
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##bcftools_viewVersion=1.9+htslib-1.9
+##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Fri Jan 18 16:21:02 2019
+##bcftools_annotateVersion=1.9+htslib-1.9
+##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Fri Jan 18 16:21:02 2019
+##INFO=<ID=OLDVAR,Number=R,Type=String,Description="Original REF,ALT before decomposition">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	out
+Wildtype	24388	.	A	G	673.635	.	TYPE=snp;DP=22;RO=0;AO=22	GT:DP:RO:AO:QR:QA	1/1:22:0:22:0:785
+Wildtype	29479	.	T	G	673.562	.	TYPE=snp;DP=21;RO=0;AO=21	GT:DP:RO:AO:QR:QA	1/1:21:0:21:0:776
+Wildtype	47299	.	T	A	772.746	.	TYPE=snp;DP=25;RO=0;AO=25	GT:DP:RO:AO:QR:QA	1/1:25:0:25:0:921
+Wildtype	102969	.	G	C	548.461	.	TYPE=snp;DP=18;RO=0;AO=18	GT:DP:RO:AO:QR:QA	1/1:18:0:18:0:637
+Wildtype	103048	.	T	A	659.012	.	TYPE=snp;DP=23;RO=0;AO=23	GT:DP:RO:AO:QR:QA	1/1:23:0:23:0:766
+Wildtype	106602	.	T	G	679.76	.	TYPE=snp;DP=22;RO=0;AO=22	GT:DP:RO:AO:QR:QA	1/1:22:0:22:0:790
+Wildtype	109833	.	T	A	523.219	.	TYPE=snp;DP=17;RO=0;AO=17	GT:DP:RO:AO:QR:QA	1/1:17:0:17:0:612
+Wildtype	129881	.	G	A	591.829	.	TYPE=snp;DP=19;RO=0;AO=19;OLDVAR=mnp,129881,GT,AA	GT:DP:RO:AO:QR:QA	1/1:19:0:19:0:686
+Wildtype	129882	.	T	A	591.829	.	TYPE=snp;DP=19;RO=0;AO=19;OLDVAR=mnp,129881,GT,AA	GT:DP:RO:AO:QR:QA	1/1:19:0:19:0:686
+Wildtype	138877	.	G	C	433.927	.	TYPE=snp;DP=14;RO=0;AO=14	GT:DP:RO:AO:QR:QA	1/1:14:0:14:0:507
+Wildtype	138954	.	A	G	302.917	.	TYPE=snp;DP=10;RO=0;AO=10	GT:DP:RO:AO:QR:QA	1/1:10:0:10:0:354