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annotate test-data/output_haplotype.out.phased.vcf @ 2:800f8086da7d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 908fb9148a3a116dbf7ccd16e0992e7882e748c2
author iuc
date Tue, 30 Apr 2024 08:38:15 +0000
parents fb00fb7cb201
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1 ##fileformat=VCFv4.2
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2 ##FILTER=<ID=PASS,Description="All filters passed">
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3 ##fileDate=20220204
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4 ##source=freeBayes v1.3.2-dirty
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5 ##reference=reference/ref.fa
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6 ##contig=<ID=NC_045512.2,length=29903>
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7 ##phasing=none
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8 ##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"
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9 ##INFO=<ID=hapcut2,Number=1,Type=Integer,Description="phased by HapCUT2 or not">
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10 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
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11 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
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12 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
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13 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
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14 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
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15 ##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">
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16 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
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17 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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18 ##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">
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19 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
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20 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
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21 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
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22 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
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23 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
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24 ##bcftools_viewVersion=1.13+htslib-1.13
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25 ##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
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26 ##bcftools_annotateVersion=1.13+htslib-1.13
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27 ##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
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28 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="ID of Phase Set for Variant">
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29 ##FORMAT=<ID=PQ,Number=1,Type=Integer,Description="Phred QV indicating probability that this variant is incorrectly phased relative to the haplotype">
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30 ##FORMAT=<ID=PD,Number=1,Type=Integer,Description="phased Read Depth">
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31 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sars_cov_2_omicron_SRR17309642_R1_25k_fastq_gz
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32 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:PS 1/1:11:0:0:11:418:-37.9727,-3.31133,0:.
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33 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:PS 1/1:15:0:0:15:570:-51.6429,-4.51545,0:.
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34 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:PS 1/1:22:0:0:22:836:-75.5656,-6.62266,0:.