view test-data/b_out_dev/snps.subs.vcf @ 21:0e733df972b5 draft

planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty

##fileformat=VCFv4.2
##snippy="snippy-vcf_extract_subs snps.filt.vcf"
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20190312
##source=freeBayes v1.2.0-dirty
##reference=reference/ref.fa
##contig=<ID=reference,length=700>
##phasing=none
##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700"
##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>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Tue Mar 12 14:35:28 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=Tue Mar 12 14:35:28 2019
##INFO=<ID=OLDVAR,Number=R,Type=String,Description="Original REF,ALT before decomposition">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	b
reference	4	.	A	T	321.326	.	TYPE=snp;DP=10;RO=0;AO=10	GT:DP:RO:AO:QR:QA	1/1:10:0:10:0:400