Mercurial > repos > iuc > gatk4_mutect2

annotate test-data/Mutect2-out5.vcf @ 3:287c4af133e6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
author iuc
date Sun, 10 May 2020 17:58:00 -0400
parents fd2d6e035c3f
children
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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">
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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; will always be heterozygous and is not intended to describe called alleles">
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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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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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14 ##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --bam-output debug.bam --output output.vcf --assembly-region-out assembly-region.tab --input tumor.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 --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 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --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 --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --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="4.1.7.0",Date="May 8, 2020 3:33:33 PM CEST">
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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15 ##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |.">
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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16 ##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site">
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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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17 ##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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18 ##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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19 ##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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20 ##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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21 ##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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22 ##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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23 ##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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24 ##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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25 ##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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26 ##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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27 ##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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28 ##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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29 ##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
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30 ##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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31 ##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
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32 ##INFO=<ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
0
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33 ##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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34 ##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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35 ##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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36 ##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
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37 ##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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38 ##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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39 ##MutectVersion=2.2
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40 ##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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41 ##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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42 ##source=Mutect2
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43 ##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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44 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881
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45 K03455 2097 . G A . . AS_SB_TABLE=0,0|10,5;DP=15;ECNT=41;MBQ=0,20;MFRL=0,159;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=79.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,15:0.929:15:0,7:0,6:0,0,10,5
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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46 K03455 2106 . T C . . AS_SB_TABLE=9,4|2,2;DP=17;ECNT=41;MBQ=20,30;MFRL=159,90;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=12.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,4:0.266:17:6,1:7,1:9,4,2,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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47 K03455 2110 . TA CA,CT . . AS_SB_TABLE=0,0|9,5|3,1;DP=18;ECNT=41;MBQ=0,20,35;MFRL=0,159,161;MMQ=60,60,60;MPOS=44,2;POPAF=7.30,7.30;TLOD=60.04,10.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:0,14,4:0.754,0.187:18:0,6,1:0,8,3:0,0,12,6
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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48 K03455 2118 . A G . . AS_SB_TABLE=3,2|8,3;DP=18;ECNT=41;MBQ=32,20;MFRL=90,160;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=35.11 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,11:0.715:16:1,4:4,6:3,2,8,3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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49 K03455 2130 . T C . . AS_SB_TABLE=9,5|3,1;DP=18;ECNT=41;MBQ=20,37;MFRL=159,161;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=10.45 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:14,4:0.199:18:4,1:9,3:9,5,3,1
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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50 K03455 2136 . T C . . AS_SB_TABLE=9,5|3,1;DP=18;ECNT=41;MBQ=20,38;MFRL=159,161;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=10.45 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:14,4:0.199:18:4,1:10,2:9,5,3,1
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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51 K03455 2155 . A T . . AS_SB_TABLE=3,2|11,4;DP=20;ECNT=41;MBQ=39,20;MFRL=90,233;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=41.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,15:0.777:20:1,5:4,7:3,2,11,4
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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52 K03455 2169 . A G . . AS_SB_TABLE=0,0|17,6;DP=23;ECNT=41;MBQ=0,34;MFRL=0,232;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=105.32 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,23:0.955:23:0,9:0,13:0,0,17,6
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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53 K03455 2183 . C T . . AS_SB_TABLE=0,0|19,9;DP=28;ECNT=41;MBQ=0,33;MFRL=0,233;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=133.75 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,28:0.962:28:0,9:0,14:0,0,19,9
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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54 K03455 2189 . TA AA,AG . . AS_SB_TABLE=0,0|9,5|10,4;DP=30;ECNT=41;MBQ=0,35,20;MFRL=0,207,265;MMQ=60,60,60;MPOS=21,22;POPAF=7.30,7.30;TLOD=51.22,55.00 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:0,14,14:0.424,0.539:28:0,6,5:0,7,5:0,0,19,9
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
55 K03455 2195 . C G,T . . AS_SB_TABLE=5,4|10,4|5,2;DP=30;ECNT=41;MBQ=37,30,33;MFRL=232,265,241;MMQ=60,60,60;MPOS=19,19;POPAF=7.30,7.30;TLOD=41.44,19.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:9,14,7:0.500,0.250:30:3,8,3:5,6,4:5,4,15,6
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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56 K03455 2197 . A G . . AS_SB_TABLE=15,6|5,4;DP=30;ECNT=41;MBQ=31,37;MFRL=248,232;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=29.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:21,9:0.259:30:9,3:8,5:15,6,5,4
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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57 K03455 2200 . ACTC A . . AS_SB_TABLE=16,8|3,2;DP=31;ECNT=41;MBQ=24,36;MFRL=265,232;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=13.22 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:24,5:0.153:29:10,3:7,2:0|1:2200_ACTC_A:2200:16,8,3,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
58 K03455 2202 . T C . . AS_SB_TABLE=15,7|2,2;DP=31;ECNT=41;MBQ=34,35;MFRL=257,182;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=5.58 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:22,4:0.166:26:9,1:7,1:0|1:2202_T_C:2202:15,7,2,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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59 K03455 2205 . C A . . AS_SB_TABLE=20,9|1,1;DP=31;ECNT=41;MBQ=34,26;MFRL=248,286;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=5.06 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:29,2:0.107:31:13,1:11,0:0|1:2202_T_C:2202:20,9,1,1
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
60 K03455 2213 . A G . . AS_SB_TABLE=4,3|17,7;DP=31;ECNT=41;MBQ=38,37;MFRL=232,265;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=107.32 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:7,24:0.793:31:4,11:2,8:4,3,17,7
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
61 K03455 2214 . G A . . AS_SB_TABLE=17,9|1,1;DP=28;ECNT=41;MBQ=33,26;MFRL=254,286;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=5.06 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:26,2:0.107:28:12,1:10,0:0|1:2214_G_A:2214:17,9,1,1
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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62 K03455 2221 . C A . . AS_SB_TABLE=22,8|3,2;DP=35;ECNT=41;MBQ=34,35;MFRL=251,232;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=12.67 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:30,5:0.114:35:16,1:11,2:0|1:2200_ACTC_A:2200:22,8,3,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
63 K03455 2223 . G A . . AS_SB_TABLE=16,3|7,7;DP=34;ECNT=41;MBQ=37,34;MFRL=253,211;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=47.83 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:19,14:0.461:33:12,7:7,6:16,3,7,7
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
64 K03455 2224 . AT GG,CT . . AS_SB_TABLE=11,8|2,2|10,0;DP=33;ECNT=41;MBQ=34,29,38;MFRL=265,207,253;MMQ=60,60,60;MPOS=36,18;POPAF=7.30,7.30;TLOD=9.64,33.76 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:19,4,10:0.091,0.333:33:9,2,7:8,2,3:11,8,12,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
65 K03455 2225 . T G . . AS_SB_TABLE=20,7|1,1;DP=33;ECNT=41;MBQ=37,38;MFRL=253,286;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=5.14 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:27,2:0.099:29:16,1:11,1:0|1:2214_G_A:2214:20,7,1,1
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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66 K03455 2226 . A G . . AS_SB_TABLE=3,3|20,7;DP=33;ECNT=41;MBQ=20,37;MFRL=232,253;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=115.36 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,27:0.844:33:3,16:2,9:0|1:2226_A_G:2226:3,3,20,7
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
67 K03455 2230 . A C . . AS_SB_TABLE=3,3|21,7;DP=34;ECNT=41;MBQ=28,37;MFRL=232,253;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=119.79 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,28:0.848:34:2,15:3,11:0|1:2226_A_G:2226:3,3,21,7
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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68 K03455 2234 . A G . . AS_SB_TABLE=3,3|24,10;DP=40;ECNT=41;MBQ=20,37;MFRL=232,245;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=146.51 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,34:0.865:40:1,20:2,11:0|1:2226_A_G:2226:3,3,24,10
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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69 K03455 2235 . AC GA . . AS_SB_TABLE=25,11|2,2;DP=40;ECNT=41;MBQ=35,33;MFRL=247,207;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=9.17 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:36,4:0.081:40:22,1:10,2:0|1:2200_ACTC_A:2200:25,11,2,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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70 K03455 2236 . CTG C,GTG . . AS_SB_TABLE=12,2|12,8|1,1;DP=40;ECNT=41;MBQ=38,35,38;MFRL=251,240,286;MMQ=60,60,60;MPOS=16,46;POPAF=7.30,7.30;TLOD=62.15,5.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:14,20,2:0.528,0.083:36:8,12,1:5,8,1:12,2,13,9
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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71 K03455 2239 . TA CC . . AS_SB_TABLE=16,11|12,2;DP=43;ECNT=41;MBQ=36,38;MFRL=232,251;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=49.19 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:27,14:0.368:41:14,9:10,4:16,11,12,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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72 K03455 2240 . A ACC . . AS_SB_TABLE=4,3|14,10;DP=43;ECNT=41;MBQ=37,34;MFRL=232,211;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=61.81 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:7,24:0.785:31:3,13:3,9:4,3,14,10
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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73 K03455 2248 . A G . . AS_SB_TABLE=3,2|27,12;DP=44;ECNT=41;MBQ=20,38;MFRL=182,245;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=182.06 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:5,39:0.902:44:2,21:3,15:1|0:2200_ACTC_A:2200:3,2,27,12
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
74 K03455 2250 . T C . . AS_SB_TABLE=27,12|3,2;DP=44;ECNT=41;MBQ=38,37;MFRL=245,182;MMQ=60,60;MPOS=60;POPAF=7.30;TLOD=12.44 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:39,5:0.098:44:23,2:16,3:0|1:2200_ACTC_A:2200:27,12,3,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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75 K03455 2258 . GG AA . . AS_SB_TABLE=6,0|26,14;DP=46;ECNT=41;MBQ=39,39;MFRL=216,239;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=159.02 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,40:0.859:46:3,22:3,17:0|1:2258_GG_AA:2258:6,0,26,14
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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76 K03455 2259 . G A . . AS_SB_TABLE=0,0|10,3;DP=46;ECNT=41;MBQ=0,37;MFRL=0,241;MMQ=60,60;MPOS=39;POPAF=7.30;TLOD=13.48 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:0,13:0.961:13:0,5:0,8:1|0:2258_GG_AA:2258:0,0,10,3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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77 K03455 2282 . C T . . AS_SB_TABLE=32,24|2,2;DP=60;ECNT=41;MBQ=36,20;MFRL=239,182;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=9.01 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:56,4:0.059:60:24,1:24,2:32,24,2,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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78 K03455 2285 . C T . . AS_SB_TABLE=30,23|6,3;DP=62;ECNT=41;MBQ=29,38;MFRL=236,205;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=26.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:53,9:0.151:62:24,3:21,4:30,23,6,3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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79 K03455 2287 . CA AT . . AS_SB_TABLE=32,26|4,3;DP=65;ECNT=41;MBQ=33,37;MFRL=234,285;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=17.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:58,7:0.133:65:25,1:24,2:32,26,4,3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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80 K03455 2300 . G A . . AS_SB_TABLE=6,6|26,23;DP=63;ECNT=41;MBQ=31,32;MFRL=229,236;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=211.84 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,49:0.796:61:3,20:5,22:6,6,26,23
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
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81 K03455 2303 . GCA G . . AS_SB_TABLE=7,8|25,20;DP=61;ECNT=41;MBQ=36,31;MFRL=225,241;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=171.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:15,45:0.735:60:2,18:9,20:7,8,25,20
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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82 K03455 2304 . CAA GTG . . AS_SB_TABLE=6,6|10,9;DP=61;ECNT=41;MBQ=33,20;MFRL=229,235;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=3.47 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,19:0.531:31:4,0:7,3:6,6,10,9
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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83 K03455 2306 . A ATG,G . . AS_SB_TABLE=2,2|26,22|4,4;DP=60;ECNT=41;MBQ=29,32,33;MFRL=182,239,280;MMQ=60,60,60;MPOS=39,19;POPAF=7.30,7.30;TLOD=175.97,22.08 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:4,48,8:0.779,0.164:60:2,20,2:2,23,4:2,2,30,26
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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84 K03455 2315 . A G . . AS_SB_TABLE=19,19|11,9;DP=59;ECNT=41;MBQ=37,38;MFRL=229,244;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=74.64 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:38,20:0.379:58:17,6:15,14:0|1:2315_A_G:2315:19,19,11,9
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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85 K03455 2321 . A C . . AS_SB_TABLE=17,19|11,9;DP=56;ECNT=41;MBQ=34,37;MFRL=229,244;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=75.24 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:36,20:0.392:56:16,6:17,14:0|1:2315_A_G:2315:17,19,11,9
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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86 K03455 2349 . T C . . AS_SB_TABLE=23,24|4,5;DP=56;ECNT=9;MBQ=35,35;MFRL=235,285;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=28.30 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:47,9:0.190:56:19,3:22,5:23,24,4,5
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
87 K03455 2360 . G A . . AS_SB_TABLE=19,20|4,6;DP=49;ECNT=9;MBQ=37,27;MFRL=235,272;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=28.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:39,10:0.229:49:15,3:22,3:19,20,4,6
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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88 K03455 2362 . G A . . AS_SB_TABLE=0,0|21,26;DP=49;ECNT=9;MBQ=0,36;MFRL=0,241;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=181.58 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,47:0.978:47:0,19:0,25:0,0,21,26
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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89 K03455 2372 . A G . . AS_SB_TABLE=16,19|4,5;DP=44;ECNT=9;MBQ=37,36;MFRL=241,259;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=30.36 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:35,9:0.234:44:9,3:17,5:16,19,4,5
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
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90 K03455 2374 . G A . . AS_SB_TABLE=12,22|2,2;DP=38;ECNT=9;MBQ=37,35;MFRL=234,284;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=7.75 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,4:0.118:38:8,1:20,2:12,22,2,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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91 K03455 2423 . A G . . AS_SB_TABLE=0,13|0,3;DP=16;ECNT=9;MBQ=34,33;MFRL=255,199;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=8.83 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,3:0.226:16:3,0:9,3:0,13,0,3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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92 K03455 2436 . A G . . AS_SB_TABLE=0,1|0,4;DP=6;ECNT=9;MBQ=16,31;MFRL=255,240;MMQ=60,60;MPOS=4;POPAF=7.30;TLOD=16.53 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,4:0.725:5:0,0:0,4:0,1,0,4
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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93 K03455 2438 . A G . . AS_SB_TABLE=0,3|0,2;DP=6;ECNT=9;MBQ=29,33;MFRL=255,255;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=7.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:3,2:0.430:5:0,0:2,2:0|1:2438_A_G:2438:0,3,0,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
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94 K03455 2440 . T C . . AS_SB_TABLE=0,3|0,2;DP=6;ECNT=9;MBQ=0,31;MFRL=255,255;MMQ=60,60;MPOS=1;POPAF=7.30;TLOD=7.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:3,2:0.430:5:0,0:0,2:0|1:2438_A_G:2438:0,3,0,2