Mercurial > repos > iuc > tb_variant_filter

annotate test-data/test_output2.vcf @ 0:3b1e7c170b10 draft

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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
author iuc
date Thu, 10 Oct 2019 17:59:02 -0400
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3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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1 ##fileformat=VCFv4.2
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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2 ##FILTER=<ID=PASS,Description="All filters passed">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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3 ##fileDate=20190323
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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4 ##source=freeBayes v1.2.0-dirty
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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5 ##reference=reference/ref.fa
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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6 ##contig=<ID=Chromosome,length=4411532>
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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7 ##phasing=none
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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8 ##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044"
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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10 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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11 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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12 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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13 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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14 ##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">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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15 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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17 ##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">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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19 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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20 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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21 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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22 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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23 ##bcftools_viewVersion=1.9+htslib-1.9
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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24 ##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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25 ##bcftools_annotateVersion=1.9+htslib-1.9
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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26 ##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=Sat Mar 23 06:45:26 2019
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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27 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT out
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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28 Chromosome 1849 . C A 3412.24 . AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:0:0:110:3850:-346.644,-33.1133,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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29 Chromosome 1977 . A G 3234.43 . AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3704:-333.508,-31.9092,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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30 Chromosome 4013 . T C 3965.91 . AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:125:4448:-400.411,-37.6288,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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31 Chromosome 7362 . G C 4009.71 . AB=0.0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4518:-406.711,-37.9298,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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32 Chromosome 9304 . G A 4222.23 . AB=0.0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4764:-428.865,-40.9401,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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33 Chromosome 11820 . C G 2252.54 . AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:74:0:0:74:2662:-239.791,-22.2762,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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34 Chromosome 11879 . A G 1815.99 . AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:63:0:0:63:2212:-199.306,-18.9649,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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35 Chromosome 14785 . T C 4342.4 . AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:139:0:0:139:4874:-438.763,-41.8432,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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36 Chromosome 14861 . G T 4237.79 . AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:135:0:0:133:4758:-427.969,-40.037,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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37 Chromosome 15117 . C G 3298.26 . AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3708:-333.903,-31.9092,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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38 Chromosome 15890 . G A 3349.13 . AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:116:3770:-339.321,-34.9195,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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39 Chromosome 16119 . C A 3794.09 . AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:124:4268:-383.905,-37.3277,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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40 Chromosome 21795 . G A 768.571 . AB=0.0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:28:0:0:28:892:-80.5646,-8.42884,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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41 Chromosome 25610 . G C 2779.82 . AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3137:-282.515,-26.7917,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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42 Chromosome 26959 . C G 2791.1 . AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:91:0:0:91:3152:-283.856,-27.3937,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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43 Chromosome 27455 . T C 1646.76 . AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:52:0:0:52:1868:-168.374,-15.6536,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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44 Chromosome 28366 . AT A 2447.14 . AB=0.0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:82:2764:-248.651,-24.6845,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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45 Chromosome 34044 . T C 3866.76 . AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4351:-391.712,-36.7257,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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46 Chromosome 36008 . G C 2942.73 . AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:0:0:98:3356:-301.935,-29.5009,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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47 Chromosome 37031 . C G 3922.6 . AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:129:1:34:128:4437:-396.072,-35.434,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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48 Chromosome 37305 . C G 4975.87 . AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:157:0:0:157:5577:-501.976,-47.2617,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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49 Chromosome 39158 . C G 2017.05 . AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:66:0:0:66:2297:-206.967,-19.868,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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50 Chromosome 42281 . C A 996.941 . AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:33:0:0:33:1179:-106.407,-9.93399,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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51 Chromosome 42967 . G C 2851.59 . AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3244:-292.146,-27.6948,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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52 Chromosome 43347 . T C 2847.24 . AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3233:-291.161,-27.6948,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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53 Chromosome 44768 . A G 3099.48 . AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:99:3501:-315.241,-29.802,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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54 Chromosome 49360 . C T 2971.13 . AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:97:0:0:97:3365:-303.059,-29.1999,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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55 Chromosome 49690 . GCC G 3479.85 . AB=0.0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:117:3917:-352.709,-35.2205,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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56 Chromosome 50557 . T C 3743.4 . AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4203:-378.409,-36.4246,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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57 Chromosome 51949 . A G 3521.52 . AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:112:0:0:112:3955:-356.092,-33.7154,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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58 Chromosome 54394 . A G 3304.32 . AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:104:3711:-333.937,-31.3071,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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59 Chromosome 62049 . A G 2249.46 . AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:1:35:77:2659:-236.018,-19.9817,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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diff changeset
60 Chromosome 63146 . G T 5120.15 . AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:163:0:0:163:5737:-516.376,-49.0679,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
61 Chromosome 65150 . C T 4046.85 . AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:134:0:0:134:4538:-408.565,-40.338,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
62 Chromosome 65246 . C T 3297.8 . AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:107:0:0:106:3712:-334.038,-31.9092,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
63 Chromosome 68337 . T TC 1791.13 . AB=0.0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:60:2038:-183.378,-18.0618,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
64 Chromosome 69989 . G A 3539.46 . AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:119:0:0:119:3973:-357.725,-35.8226,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
65 Chromosome 70267 . G T 3018.85 . AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:1:25:100:3421:-305.576,-27.9042,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
66 Chromosome 70816 . A G 4198.57 . AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4707:-423.747,-40.9401,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
67 Chromosome 71336 . G C 556.161 . AB=0.0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:21:0:0:21:770:-69.6143,-6.32163,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
68 Chromosome 71914 . T C 3905.06 . AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4382:-394.523,-37.9298,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
69 Chromosome 75233 . C A 1903.61 . AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2172:-195.723,-19.2659,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
70 Chromosome 75940 . G C 2674.83 . AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3048:-274.519,-26.7917,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
71 Chromosome 87468 . C T 4061.4 . AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4584:-412.628,-37.9298,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
72 Chromosome 92199 . T G 686.38 . AB=0.0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:23:0:0:23:799:-72.2155,-6.92369,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
73 Chromosome 94388 . G A 2922.87 . AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:95:0:0:95:3292:-296.486,-28.5979,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
74 Chromosome 99162 . TCGGTGTGCG T 2040.99 . AB=0.0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2358:-212.453,-23.4803,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
75 Chromosome 105139 . C A 3418.74 . AB=0.0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:1:38:109:3888:-346.257,-29.316,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
76 Chromosome 105736 . T C 1805.18 . AB=0.0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:61:2101:-189.335,-18.3628,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
77 Chromosome 116000 . T G 3196.37 . AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3605:-324.628,-31.6082,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
78 Chromosome 122109 . A G 3324.29 . AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:111:0:0:111:3735:-336.329,-33.4143,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
79 Chromosome 123454 . C T 4362.28 . AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:136:4894:-440.321,-40.9401,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
80 Chromosome 123520 . T C 3793.13 . AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4262:-383.682,-36.4246,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
81 Chromosome 125711 . GGTT G 3140.7 . AB=0.0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3531:-317.98,-31.6082,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
82 Chromosome 125830 . G GA 2079.98 . AB=0.0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:69:2347:-211.164,-20.7711,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
83 Chromosome 131174 . T TG 2854.04 . AB=0.0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:97:3213:-288.972,-29.1999,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
84 Chromosome 133839 . C T 2457.55 . AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2802:-252.374,-23.4803,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
85 Chromosome 134024 . T C 2242.53 . AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2543:-229.099,-21.6742,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
86 Chromosome 138419 . G A 4166.36 . AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:132:0:0:132:4683:-421.582,-39.736,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
87 Chromosome 139297 . G T 3706.81 . AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:120:0:0:120:4165:-374.978,-36.1236,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
88 Chromosome 143207 . T C 2180.95 . AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2523:-227.3,-21.6742,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
89 Chromosome 146087 . T C 4315.28 . AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:137:4844:-436.07,-41.2411,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
90 Chromosome 147262 . G T 3766.49 . AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4228:-380.649,-36.7257,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
91 Chromosome 154283 . T C 4403.08 . AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:141:0:0:141:4941:-444.791,-42.4452,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
92 Chromosome 154990 . G T 4207.92 . AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:143:0:0:142:4724:-424.969,-42.7463,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
93 Chromosome 162151 . GT G 2208.67 . AB=0.0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:81:2524:-226.95,-24.3834,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
94 Chromosome 163940 . A G 2507.97 . AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:80:0:0:80:2839:-255.719,-24.0824,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
95 Chromosome 166253 . A C 3141.13 . AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:102:0:0:102:3586:-322.902,-30.7051,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
96 Chromosome 177857 . G A 2984.02 . AB=0.0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:98:0:0:98:3389:-305.192,-29.5009,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
97 Chromosome 188800 . T C 1887.67 . AB=0.0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2217:-199.772,-19.2659,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
98 Chromosome 190816 . A C 1715.49 . AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:57:0:0:57:2026:-182.579,-17.1587,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
99 Chromosome 194305 . C CGG 1602.78 . AB=0.0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:59:0:0:58:1889:-169.924,-17.4597,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
100 Chromosome 2738274 . A C 511.15 . AB=0.0;AO=18;DP=19;QA=633;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:19:1:35:18:633:-53.7923,-2.22094,0.0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff changeset
101 Chromosome 3750185 . CGAC GGTG 1102.73 . AB=0.0;AO=36;DP=36;QA=1255;QR=0;RO=0;TYPE=complex GT:DP:RO:QR:AO:QA:GL 1/1:36:0:0:36:1255:-113.24,-10.8371,0.0