annotate test-data/input.vcf @ 0:fb00fb7cb201 draft

"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7770c3ea0fab9df0f39d3d73d10c9e282b77c60f-dirty"

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20220204
##source=freeBayes v1.3.2-dirty
##reference=reference/ref.fa
##contig=<ID=NC_045512.2,length=29903>
##phasing=none
##commandline="freebayes -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam --region NC_045512.2:0-2772"
##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=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
##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=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##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=1.13+htslib-1.13
##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Fri Feb  4 01:38:26 2022
##bcftools_annotateVersion=1.13+htslib-1.13
##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 Feb  4 01:38:27 2022
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sars_cov_2_omicron_SRR17309642_R1_25k_fastq_gz
NC_045512.2	3037	.	C	T	338.161	.	AB=0;AO=11;DP=11;QA=418;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:418:-37.9727,-3.31133,0
NC_045512.2	14408	.	C	T	494.13	.	AB=0;AO=15;DP=15;QA=570;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:570:-51.6429,-4.51545,0
NC_045512.2	23403	.	A	G	716.256	.	AB=0;AO=22;DP=22;QA=836;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:836:-75.5656,-6.62266,0