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annotate test-data/c/snps.subs.vcf @ 20:3bbfe41787af draft

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planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
author dfornika
date Fri, 08 Mar 2019 20:46:56 -0500
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1 ##fileformat=VCFv4.2
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2 ##snippy="snippy-vcf_extract_subs snps.filt.vcf"
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3 ##fileformat=VCFv4.2
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4 ##FILTER=<ID=PASS,Description="All filters passed">
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5 ##fileDate=20190206
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6 ##source=freeBayes v1.2.0-dirty
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7 ##reference=reference/ref.fa
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8 ##contig=<ID=reference,length=700>
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9 ##phasing=none
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10 ##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"
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11 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
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12 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
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13 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
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14 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
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15 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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16 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
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17 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
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18 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
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19 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
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20 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
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21 ##bcftools_viewVersion=1.9+htslib-1.9
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22 ##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 12:42:19 2019
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23 ##bcftools_annotateVersion=1.9+htslib-1.9
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24 ##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=Wed Feb 6 12:42:19 2019
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25 ##INFO=<ID=OLDVAR,Number=R,Type=String,Description="Original REF,ALT before decomposition">
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26 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT c
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27 reference 48 . A C 63.8794 . TYPE=snp;DP=2;RO=0;AO=2 GT:DP:RO:AO:QR:QA 1/1:2:0:2:0:80