Mercurial > repos > galaxy-australia > hapcut2
diff test-data/input.vcf @ 0:fb00fb7cb201 draft
"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7770c3ea0fab9df0f39d3d73d10c9e282b77c60f-dirty"
| author | galaxy-australia |
|---|---|
| date | Wed, 27 Apr 2022 06:34:22 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.vcf Wed Apr 27 06:34:22 2022 +0000 @@ -0,0 +1,30 @@ +##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