Mercurial > repos > iuc > gatk4_mutect2

annotate test-data/Mutect2-out2.vcf @ 1:fd2d6e035c3f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
author iuc
date Mon, 18 Nov 2019 13:45:47 -0500
parents f41a1e03538b
children 287c4af133e6
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f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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1 ##fileformat=VCFv4.2
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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2 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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3 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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5 ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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6 ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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7 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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8 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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9 ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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10 ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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11 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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12 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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13 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
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fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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14 ##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input input.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="November 15, 2019 4:25:08 PM EST">
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f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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15 ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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16 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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17 ##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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18 ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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19 ##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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20 ##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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21 ##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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22 ##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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23 ##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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24 ##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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25 ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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26 ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig.">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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27 ##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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28 ##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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29 ##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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30 ##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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31 ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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32 ##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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33 ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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34 ##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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35 ##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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36 ##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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37 ##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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38 ##MutectVersion=2.2
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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39 ##contig=<ID=K03455,length=9719>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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40 ##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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41 ##source=Mutect2
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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42 ##tumor_sample=SRR8525881
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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43 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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44 K03455 4861 . A G . . DP=1;ECNT=13;MBQ=0,37;MFRL=0,400;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=3.88 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,1:0,0:0,0,1,0
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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45 K03455 4918 . G A . . DP=10;ECNT=13;MBQ=37,32;MFRL=282,328;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=17.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:4,6:0.583:10:2,1:2,3:3,1,1,5
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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46 K03455 4923 . A G . . DP=11;ECNT=13;MBQ=0,33;MFRL=0,303;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=50.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,11:0.923:11:0,4:0,5:0,0,5,6
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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47 K03455 4949 . G A . . DP=16;ECNT=13;MBQ=38,37;MFRL=281,279;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=40.32 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,10:0.647:16:2,3:2,6:0|1:4949_G_A:4949:3,3,4,6
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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48 K03455 4952 . C T . . DP=18;ECNT=13;MBQ=25,37;MFRL=281,279;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=40.30 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,10:0.647:16:2,3:2,7:0|1:4949_G_A:4949:3,3,4,6
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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49 K03455 4988 . T C . . DP=32;ECNT=13;MBQ=34,35;MFRL=261,290;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=23.96 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:24,8:0.258:32:9,4:12,3:12,12,4,4
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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50 K03455 4991 . T C . . DP=32;ECNT=13;MBQ=33,20;MFRL=264,292;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=6.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:29,3:0.128:32:13,1:15,1:15,14,1,2
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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51 K03455 4996 . AC GA . . DP=36;ECNT=13;MBQ=37,26;MFRL=264,256;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=11.76 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:29,6:0.181:35:10,2:12,3:14,15,3,3
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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52 K03455 4997 . C T,A . . DP=36;ECNT=13;MBQ=20,20,38;MFRL=278,131,257;MMQ=60,60,60;MPOS=10,31;POPAF=7.30,7.30;TLOD=14.89,42.60 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:11,5,19:0.149,0.553:35:6,1,7:3,3,12:6,5,11,13
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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53 K03455 5015 . A G . . DP=49;ECNT=13;MBQ=27,37;MFRL=245,251;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=126.23 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:14,32:0.721:46:7,8:6,23:6,8,14,18
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
54 K03455 5018 . A G . . DP=49;ECNT=13;MBQ=33,20;MFRL=257,180;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=14.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:43,6:0.129:49:13,1:21,5:19,24,2,4
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
55 K03455 5027 . G A . . DP=54;ECNT=13;MBQ=33,20;MFRL=254,158;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=16.84 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:46,7:0.148:53:15,1:25,6:0|1:5027_G_A:5027:19,27,2,5
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
56 K03455 5036 . G A . . DP=53;ECNT=13;MBQ=32,20;MFRL=251,158;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=16.91 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:45,7:0.151:52:17,1:25,5:0|1:5027_G_A:5027:19,26,2,5
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
57 K03455 5076 . A G . . DP=49;ECNT=29;MBQ=36,20;MFRL=260,210;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=15.53 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:43,6:0.151:49:12,1:28,5:0|1:5076_A_G:5076:11,32,0,6
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
58 K03455 5098 . A G . . DP=55;ECNT=29;MBQ=20,32;MFRL=210,269;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=180.82 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:8,46:0.816:54:0,9:7,26:0,8,10,36
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
59 K03455 5099 . C T . . DP=55;ECNT=29;MBQ=33,20;MFRL=269,210;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=22.21 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:46,8:0.183:54:8,1:31,6:0|1:5076_A_G:5076:10,36,0,8
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
60 K03455 5121 . C T . . DP=55;ECNT=29;MBQ=20,20;MFRL=251,245;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=54.15 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:39,16:0.265:55:7,5:30,9:6,33,4,12
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
61 K03455 5130 . TG CA . . DP=49;ECNT=29;MBQ=20,37;MFRL=205,251;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=145.65 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:14,35:0.739:49:4,4:8,29:3,11,3,32
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
62 K03455 5131 . G A . . DP=49;ECNT=29;MBQ=0,20;MFRL=0,205;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=53.22 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,14:0.951:14:0,3:0,9:0,0,3,11
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
63 K03455 5133 . T C . . DP=46;ECNT=29;MBQ=35,36;MFRL=285,219;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=31.79 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:36,10:0.251:46:6,1:26,8:0|1:5133_T_C:5133:5,31,0,10
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
64 K03455 5137 . GG AG,AA . . DP=45;ECNT=29;MBQ=26,39,39;MFRL=205,219,309;MMQ=60,60,60;MPOS=36,37;POPAF=7.30,7.30;TLOD=32.04,80.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:14,10,21:0.246,0.487:45:4,1,3:9,8,16:3,11,1,30
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
65 K03455 5146 . AGG A . . DP=43;ECNT=29;MBQ=38,37;MFRL=278,219;MMQ=60,60;MPOS=45;POPAF=7.30;RPA=4,2;RU=G;STR;TLOD=32.02 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:33,10:0.261:43:6,1:24,9:0|1:5133_T_C:5133:4,29,0,10
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
66 K03455 5147 . G A . . DP=43;ECNT=29;MBQ=20,38;MFRL=205,331;MMQ=60,60;MPOS=46;POPAF=7.30;TLOD=75.96 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:14,19:0.626:33:4,2:9,13:0|1:5147_G_A:5147:3,11,1,18
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
67 K03455 5149 . G A . . DP=42;ECNT=29;MBQ=37,18;MFRL=254,64;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=4.70 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:40,2:0.049:42:6,0:28,1:3,37,1,1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
68 K03455 5153 . GGTTT G . . DP=40;ECNT=29;MBQ=34,37;MFRL=269,219;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=32.44 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:30,10:0.281:40:6,1:22,9:0|1:5133_T_C:5133:3,27,0,10
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
69 K03455 5155 . T C . . DP=39;ECNT=29;MBQ=20,38;MFRL=181,315;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=63.73 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:13,16:0.608:29:4,2:8,13:0|1:5147_G_A:5147:3,10,0,16
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
70 K03455 5156 . T A . . DP=39;ECNT=29;MBQ=37,33;MFRL=296,260;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=39.44 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:18,11:0.356:29:2,4:16,7:0|1:5156_T_A:5156:1,17,2,9
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
71 K03455 5157 . T G,C . . DP=39;ECNT=29;MBQ=20,37,20;MFRL=260,315,64;MMQ=60,60,60;MPOS=56,5;POPAF=7.30,7.30;TLOD=63.79,5.70 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:11,16,2:0.591,0.064:29:4,2,0:7,14,2:2,9,1,17
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
72 K03455 5169 . C T . . DP=29;ECNT=29;MBQ=38,32;MFRL=275,190;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=39.25 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:18,11:0.379:29:2,4:15,7:1,17,1,10
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
73 K03455 5175 . A T . . DP=26;ECNT=29;MBQ=36,38;MFRL=222,293;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=52.80 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:13,13:0.481:26:3,2:9,11:0|1:5147_G_A:5147:0,13,1,12
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
74 K03455 5177 . G C . . DP=25;ECNT=29;MBQ=37,37;MFRL=293,219;MMQ=60,60;MPOS=58;POPAF=7.30;TLOD=28.74 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:17,8:0.346:25:4,1:12,7:0|1:5133_T_C:5133:1,16,0,8
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
75 K03455 5179 . CC AC,AA . . DP=24;ECNT=29;MBQ=38,34,38;MFRL=339,219,296;MMQ=60,60,60;MPOS=58,51;POPAF=7.30,7.30;TLOD=29.12,49.40 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:4,8,12:0.346,0.462:24:2,1,2:2,7,10:0,4,1,19
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
76 K03455 5189 . G A . . DP=25;ECNT=29;MBQ=39,39;MFRL=222,296;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=48.64 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,12:0.462:25:4,2:9,10:1,12,1,11
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
77 K03455 5190 . A G . . DP=25;ECNT=29;MBQ=39,20;MFRL=252,278;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=15.35 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:20,5:0.231:25:3,2:17,2:0|1:5156_T_A:5156:1,19,1,4
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
78 K03455 5196 . T C . . DP=25;ECNT=29;MBQ=38,20;MFRL=246,339;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=6.08 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:21,4:0.191:25:3,3:18,1:1,20,1,3
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
79 K03455 5220 . G A . . DP=23;ECNT=29;MBQ=37,37;MFRL=286,222;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=24.08 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:16,7:0.344:23:5,1:11,6:0|1:5220_G_A:5220:2,14,0,7
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
80 K03455 5223 . T A . . DP=22;ECNT=29;MBQ=37,37;MFRL=257,278;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=17.15 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:17,5:0.269:22:2,3:14,2:0|1:5223_T_A:5223:1,16,1,4
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
81 K03455 5226 . T C . . DP=22;ECNT=29;MBQ=34,35;MFRL=268,253;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=12.23 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:16,6:0.231:22:4,1:12,5:1,15,1,5
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
82 K03455 5230 . T C . . DP=21;ECNT=29;MBQ=33,38;MFRL=275,278;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=17.08 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:16,5:0.281:21:2,3:13,2:0|1:5223_T_A:5223:1,15,1,4
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
83 K03455 5233 . G A . . DP=16;ECNT=29;MBQ=38,38;MFRL=293,216;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=17.95 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:11,5:0.369:16:3,0:7,5:0|1:5220_G_A:5220:2,9,0,5
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
84 K03455 5236 . A G . . DP=16;ECNT=29;MBQ=37,38;MFRL=216,293;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=40.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,11:0.631:16:0,4:5,6:0,5,2,9
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
85 K03455 5240 . C T . . DP=15;ECNT=29;MBQ=37,37;MFRL=250,162;MMQ=60,60;MPOS=-1;POPAF=7.30;TLOD=9.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,3:0.250:15:3,0:8,3:2,10,0,3
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
86 K03455 6902 . A C . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
87 K03455 6905 . A G . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
88 K03455 6911 . T C . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
89 K03455 6917 . G A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
90 K03455 6920 . G A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
91 K03455 6923 . C T . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
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92 K03455 6931 . C A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
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93 K03455 6936 . C G . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1