Mercurial > repos > iuc > tbvcfreport

annotate test-data/rif_resistant.vcf @ 0:02d81b994ef5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
author iuc
date Thu, 29 Aug 2019 08:18:59 -0400
parents
children 42818629ec4c
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02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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1 ##fileformat=VCFv4.2
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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2 ##FILTER=<ID=PASS,Description="All filters passed">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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3 ##bcftoolsVersion=1.9+htslib-1.9
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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4 ##bcftoolsCommand=mpileup --fasta-ref /home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa rif_resistant.bam
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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5 ##reference=file:///home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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6 ##contig=<ID=MT_H37RV_BRD_V5,length=4411532>
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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7 ##ALT=<ID=*,Description="Represents allele(s) other than observed.">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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8 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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9 ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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10 ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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11 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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12 ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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13 ##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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14 ##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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15 ##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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16 ##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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17 ##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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18 ##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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19 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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20 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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21 ##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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22 ##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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23 ##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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24 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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25 ##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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26 ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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27 ##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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28 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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29 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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30 ##bcftools_callVersion=1.9+htslib-1.9
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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31 ##bcftools_callCommand=call --ploidy 1 -c -v rif_resistant.mpileup; Date=Tue Apr 2 06:47:33 2019
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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32 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT rif_resistant.bam
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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33 MT_H37RV_BRD_V5 15890 . G A 225.007 . DP=58;VDB=0.0163018;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,24;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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34 MT_H37RV_BRD_V5 154990 . G T 225.007 . DP=57;VDB=0.997362;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,18,38;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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35 MT_H37RV_BRD_V5 346693 . G T 225.007 . DP=27;VDB=0.365109;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,14,12;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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36 MT_H37RV_BRD_V5 449194 . G A 225.007 . DP=29;VDB=0.387982;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,5,21;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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37 MT_H37RV_BRD_V5 497491 . G A 225.007 . DP=78;VDB=0.57291;SGB=-0.693147;MQSB=0.99133;MQ0F=0;AF1=1;AC1=1;DP4=0,0,53,24;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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38 MT_H37RV_BRD_V5 761110 . A T 225.007 . DP=59;VDB=0.35459;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,32;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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39 MT_H37RV_BRD_V5 763031 . T C 225.007 . DP=85;VDB=0.401561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,46;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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40 MT_H37RV_BRD_V5 811753 . C T 225.007 . DP=55;VDB=0.241716;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,27,24;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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41 MT_H37RV_BRD_V5 1565566 . C T 225.007 . DP=52;VDB=0.650985;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,13,36;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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42 MT_H37RV_BRD_V5 1833729 . TCCCC TCCCCCC 12.7055 . INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AF1=1;AC1=1;DP4=0,0,0,1;MQ=54;FQ=-999 GT:PL 1:50,3,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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43 MT_H37RV_BRD_V5 1834177 . A C 225.007 . DP=76;VDB=0.880419;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,42,29;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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44 MT_H37RV_BRD_V5 1849051 . C T 225.007 . DP=86;VDB=0.199205;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,45;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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45 MT_H37RV_BRD_V5 2505085 . G A 225.007 . DP=48;VDB=0.280048;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,32,13;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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46 MT_H37RV_BRD_V5 2543395 . T C 225.007 . DP=88;VDB=0.167176;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,37,46;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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47 MT_H37RV_BRD_V5 2640807 . G A 225.007 . DP=55;VDB=0.218547;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,21;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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48 MT_H37RV_BRD_V5 2775361 . C T 225.007 . DP=99;VDB=0.0864314;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,46,44;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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49 MT_H37RV_BRD_V5 2789798 . G T 225.007 . DP=72;VDB=0.231858;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,35;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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50 MT_H37RV_BRD_V5 3477942 . A G 225.007 . DP=100;VDB=0.912557;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,45,52;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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51 MT_H37RV_BRD_V5 3587446 . G A 225.007 . DP=59;VDB=0.0078857;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,24;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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52 MT_H37RV_BRD_V5 4254431 . G A 225.007 . DP=58;VDB=0.120561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,33;MQ=60;FQ=-999 GT:PL 1:255,0
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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53 MT_H37RV_BRD_V5 4254477 . T C 225.007 . DP=30;VDB=0.000342098;SGB=-0.693021;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,10,17;MQ=60;FQ=-999 GT:PL 1:255,0