Mercurial > repos > iuc > gatk4_mutect2

annotate test-data/Mutect2-out1.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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iuc
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14 ##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --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 3:30:52 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">
0
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">
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=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
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=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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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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 4098 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;MBQ=0,34;MFRL=0,158;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=3.58 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,1:0,0,1,0
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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46 K03455 4145 . T C . . AS_SB_TABLE=0,0|3,1;DP=4;ECNT=13;MBQ=0,27;MFRL=0,242;MMQ=60,60;MPOS=39;POPAF=7.30;TLOD=17.40 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,4:0.800:4:0,1:0,3:0,0,3,1
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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47 K03455 4190 . A G . . AS_SB_TABLE=2,0|11,2;DP=15;ECNT=13;MBQ=38,37;MFRL=290,303;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=54.51 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:2,13:0.800:15:0,4:1,9:0|1:4190_A_G:4190:2,0,11,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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48 K03455 4209 . GC AC,AA . . AS_SB_TABLE=1,0|4,0|13,2;DP=20;ECNT=13;MBQ=37,35,36;MFRL=200,295,303;MMQ=60,60,60;MPOS=10,36;POPAF=7.30,7.30;TLOD=13.46,61.35 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:1,4,15:0.238,0.667:20:1,2,4:0,2,11:1,0,17,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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49 K03455 4233 . T C . . AS_SB_TABLE=18,4|5,1;DP=28;ECNT=13;MBQ=38,39;MFRL=267,268;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=19.09 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:22,6:0.261:28:7,2:13,4:1|0:4190_A_G:4190:18,4,5,1
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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50 K03455 4250 . G A . . AS_SB_TABLE=32,5|2,2;DP=42;ECNT=13;MBQ=37,28;MFRL=281,206;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=6.73 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,4:0.124:41:16,3:19,1:32,5,2,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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51 K03455 4259 . T A . . AS_SB_TABLE=7,1|30,6;DP=45;ECNT=13;MBQ=35,35;MFRL=259,280;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=151.55 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:8,36:0.786:44:3,17:5,15:0|1:4259_T_A:4259:7,1,30,6
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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52 K03455 4262 . A T . . AS_SB_TABLE=30,6|7,1;DP=45;ECNT=13;MBQ=37,37;MFRL=280,259;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=26.50 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:36,8:0.214:44:18,3:15,4:1|0:4259_T_A:4259:30,6,7,1
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
53 K03455 4268 . G A . . AS_SB_TABLE=24,7|14,0;DP=45;ECNT=13;MBQ=37,38;MFRL=272,276;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=50.83 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,14:0.349:45:12,8:15,5:24,7,14,0
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
54 K03455 4271 . A G . . AS_SB_TABLE=31,7|10,0;DP=48;ECNT=13;MBQ=37,33;MFRL=259,311;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=33.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:38,10:0.239:48:15,7:18,2:31,7,10,0
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 4277 . C T . . AS_SB_TABLE=10,2|34,6;DP=52;ECNT=13;MBQ=37,37;MFRL=244,280;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=167.14 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:12,40:0.755:52:3,20:5,18:0|1:4259_T_A:4259:10,2,34,6
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
56 K03455 4279 . GT AC,AT . . AS_SB_TABLE=17,2|18,4|9,2;DP=53;ECNT=13;MBQ=36,33,37;MFRL=263,229,272;MMQ=60,60,60;MPOS=34,39;POPAF=7.30,7.30;TLOD=61.69,29.10 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:19,22,11:0.411,0.216:52:8,9,6:9,9,5:17,2,27,6
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
57 K03455 4283 . T C . . AS_SB_TABLE=44,7|2,1;DP=54;ECNT=13;MBQ=35,37;MFRL=272,254;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=6.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:51,3:0.078:54:24,1:23,2:44,7,2,1
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 4310 . C T . . AS_SB_TABLE=25,14|4,3;DP=47;ECNT=15;MBQ=20,20;MFRL=252,254;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=18.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:39,7:0.171:46:21,1:13,4:25,14,4,3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
59 K03455 4313 . G A . . AS_SB_TABLE=26,16|2,1;DP=45;ECNT=15;MBQ=26,20;MFRL=252,200;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.55 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:42,3:0.073:45:18,1:15,1:26,16,2,1
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 4320 . G A . . AS_SB_TABLE=19,14|6,5;DP=45;ECNT=15;MBQ=20,20;MFRL=252,254;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=46.17 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:33,11:0.263:44:17,1:13,6:19,14,6,5
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 4330 . A G . . AS_SB_TABLE=25,19|3,1;DP=49;ECNT=15;MBQ=20,38;MFRL=250,276;MMQ=60,60;MPOS=60;POPAF=7.30;TLOD=13.53 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:44,4:0.111:48:19,3:20,0:25,19,3,1
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
62 K03455 4334 . A G . . AS_SB_TABLE=27,18|1,4;DP=50;ECNT=15;MBQ=33,36;MFRL=252,254;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=14.29 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:45,5:0.133:50:20,2:22,3:27,18,1,4
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 4340 . A G . . AS_SB_TABLE=15,9|12,15;DP=52;ECNT=15;MBQ=33,20;MFRL=259,252;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=102.69 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:24,27:0.511:51:11,13:12,11:0|1:4340_A_G:4340:15,9,12,15
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 4343 . C A . . AS_SB_TABLE=15,9|11,15;DP=50;ECNT=15;MBQ=33,20;MFRL=259,229;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=102.69 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:24,26:0.511:50:9,12:9,10:0|1:4340_A_G:4340:15,9,11,15
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 4345 . GC AT . . AS_SB_TABLE=21,19|7,7;DP=54;ECNT=15;MBQ=20,37;MFRL=218,251;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=54.30 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:40,14:0.277:54:14,5:15,8:21,19,7,7
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
66 K03455 4346 . C T . . AS_SB_TABLE=17,18|3,1;DP=53;ECNT=15;MBQ=20,26;MFRL=202,276;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=13.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:35,4:0.130:39:13,2:11,0:17,18,3,1
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 4358 . T C . . AS_SB_TABLE=21,22|2,5;DP=51;ECNT=15;MBQ=20,35;MFRL=229,254;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=17.73 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:43,7:0.159:50:15,4:22,3:21,22,2,5
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
68 K03455 4361 . GCT G,ACT . . AS_SB_TABLE=6,3|7,8|11,17;DP=52;ECNT=15;MBQ=36,33,20;MFRL=229,247,208;MMQ=60,60,60;MPOS=32,32;POPAF=7.30,7.30;TLOD=56.30,98.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:9,15,28:0.277,0.532:52:5,4,9:3,9,13:6,3,18,25
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
69 K03455 4364 . A AAG . . AS_SB_TABLE=17,20|7,8;DP=54;ECNT=15;MBQ=33,33;MFRL=209,247;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=55.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,15:0.282:52:17,4:18,9:17,20,7,8
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
70 K03455 4370 . A G . . AS_SB_TABLE=17,17|7,14;DP=56;ECNT=15;MBQ=20,37;MFRL=199,290;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=63.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,21:0.439:55:9,9:16,12:17,17,7,14
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
71 K03455 4376 . C T . . AS_SB_TABLE=10,19|13,13;DP=57;ECNT=15;MBQ=37,20;MFRL=252,244;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=86.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:29,26:0.437:55:9,10:16,13:10,19,13,13
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
72 K03455 4397 . T C . . AS_SB_TABLE=18,19|13,10;DP=66;ECNT=15;MBQ=33,34;MFRL=281,247;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=82.73 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,23:0.394:60:10,9:21,12:18,19,13,10
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
73 K03455 4416 . C T . . AS_SB_TABLE=22,34|6,6;DP=68;ECNT=21;MBQ=37,37;MFRL=270,305;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=37.06 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:56,12:0.197:68:20,5:33,4:22,34,6,6
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 4418 . A G . . AS_SB_TABLE=26,38|1,2;DP=67;ECNT=21;MBQ=37,37;MFRL=284,229;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=6.77 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:64,3:0.062:67:24,3:35,0:26,38,1,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
75 K03455 4421 . T C . . AS_SB_TABLE=11,20|16,20;DP=67;ECNT=21;MBQ=34,38;MFRL=263,291;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=142.09 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,36:0.538:67:16,14:12,21:11,20,16,20
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
76 K03455 4424 . T C . . AS_SB_TABLE=13,24|13,15;DP=65;ECNT=21;MBQ=37,38;MFRL=254,295;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=102.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,28:0.444:65:15,9:15,17:13,24,13,15
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
77 K03455 4430 . T C . . AS_SB_TABLE=25,37|1,2;DP=65;ECNT=21;MBQ=37,36;MFRL=280,300;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=7.02 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:62,3:0.063:65:26,2:32,1:25,37,1,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
78 K03455 4439 . A G . . AS_SB_TABLE=22,31|3,4;DP=60;ECNT=21;MBQ=38,35;MFRL=287,210;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=21.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:53,7:0.121:60:23,3:26,4:22,31,3,4
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
79 K03455 4442 . AG GA . . AS_SB_TABLE=21,30|3,4;DP=59;ECNT=21;MBQ=37,33;MFRL=287,209;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=18.12 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:51,7:0.142:58:20,2:25,5:21,30,3,4
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
80 K03455 4443 . G A . . AS_SB_TABLE=12,19|11,12;DP=59;ECNT=21;MBQ=35,38;MFRL=276,291;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=78.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,23:0.421:54:14,10:13,10:12,19,11,12
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
81 K03455 4448 . C A . . AS_SB_TABLE=22,31|1,2;DP=57;ECNT=21;MBQ=37,20;MFRL=287,126;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=8.91 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:53,3:0.055:56:21,0:27,2:22,31,1,2
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
82 K03455 4449 . C T . . AS_SB_TABLE=13,16|11,15;DP=55;ECNT=21;MBQ=37,38;MFRL=209,322;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=97.76 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:29,26:0.491:55:11,12:16,13:13,16,11,15
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
83 K03455 4460 . T C . . AS_SB_TABLE=22,22|2,5;DP=51;ECNT=21;MBQ=37,37;MFRL=279,321;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=22.02 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:44,7:0.163:51:17,3:24,3:22,22,2,5
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
84 K03455 4465 . T TGGCC . . AS_SB_TABLE=19,20|4,4;DP=50;ECNT=21;MBQ=37,35;MFRL=290,176;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=26.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:39,8:0.155:47:14,6:22,1:19,20,4,4
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
85 K03455 4466 . A G,AGTG . . AS_SB_TABLE=16,17|2,3|4,4;DP=49;ECNT=21;MBQ=37,38,37;MFRL=310,207,176;MMQ=60,60,60;MPOS=20,25;POPAF=7.30,7.30;TLOD=15.50,28.09 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:33,5,8:0.154,0.179:46:12,1,6:16,4,1:16,17,6,7
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
86 K03455 4478 . T C . . AS_SB_TABLE=12,13|5,6;DP=36;ECNT=21;MBQ=37,32;MFRL=323,205;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=44.55 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:25,11:0.306:36:9,6:15,4:12,13,5,6
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 4505 . A G . . AS_SB_TABLE=2,1|11,6;DP=20;ECNT=21;MBQ=39,37;MFRL=394,323;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=72.12 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:3,17:0.818:20:2,6:1,8:2,1,11,6
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
88 K03455 4508 . A T . . AS_SB_TABLE=2,3|10,3;DP=18;ECNT=21;MBQ=39,35;MFRL=287,335;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=52.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,13:0.700:18:3,5:2,8:2,3,10,3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
89 K03455 4511 . G A . . AS_SB_TABLE=2,1|10,5;DP=18;ECNT=21;MBQ=37,35;MFRL=394,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=62.74 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:3,15:0.800:18:2,5:1,7:2,1,10,5
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 1
diff changeset
90 K03455 4526 . T C . . AS_SB_TABLE=0,0|11,2;DP=13;ECNT=21;MBQ=0,36;MFRL=0,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=57.35 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,13:0.933:13:0,7:0,6:0,0,11,2
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 4528 . T TCA . . AS_SB_TABLE=10,1|1,1;DP=13;ECNT=21;MBQ=38,37;MFRL=323,421;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=5.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:11,2:0.200:13:5,1:4,1:0|1:4528_T_TCA:4528:10,1,1,1
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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92 K03455 4530 . CTT C . . AS_SB_TABLE=9,1|1,1;DP=13;ECNT=21;MBQ=35,38;MFRL=323,421;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=4,2;RU=T;STR;TLOD=6.12 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:10,2:0.213:12:5,1:4,1:0|1:4528_T_TCA:4528:9,1,1,1
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
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93 K03455 4532 . T C . . AS_SB_TABLE=0,0|11,0;DP=13;ECNT=21;MBQ=0,27;MFRL=0,323;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=39.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,11:0.926:11:0,6:0,2:0,0,11,0