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annotate gatk2_annotations.txt.sample @ 5:c2645201ffae draft

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author iuc
date Tue, 11 Mar 2014 07:42:09 -0400
parents 9ad15075b9fa
children b80301676614
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1 #unique_id name gatk_value tools_valid_for
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2 #http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk
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3 AlleleBalance AlleleBalance AB UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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4 AlleleBalanceBySample AlleleBalanceBySample AlleleBalanceBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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5 BaseCounts BaseCounts BaseCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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6 BaseQualityRankSumTest BaseQualityRankSumTest BaseQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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7 ChromosomeCounts ChromosomeCounts ChromosomeCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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8 Coverage Coverage Coverage UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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9 DepthPerAlleleBySample DepthPerAlleleBySample DepthPerAlleleBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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10 FisherStrand FisherStrand FisherStrand UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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11 GCContent GCContent GCContent UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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12 HaplotypeScore HaplotypeScore HaplotypeScore UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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13 HardyWeinberg HardyWeinberg HardyWeinberg UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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14 HomopolymerRun HomopolymerRun HomopolymerRun UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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15 InbreedingCoeff InbreedingCoeff InbreedingCoeff UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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16 IndelType IndelType IndelType UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
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17 LowMQ LowMQ LowMQ UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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18 MVLikelihoodRatio MVLikelihoodRatio MVLikelihoodRatio VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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19 MappingQualityRankSumTest MappingQualityRankSumTest MappingQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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20 MappingQualityZero MappingQualityZero MappingQualityZero UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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21 MappingQualityZeroBySample MappingQualityZeroBySample MappingQualityZeroBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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22 NBaseCount NBaseCount NBaseCount UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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23 QualByDepth QualByDepth QualByDepth UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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24 RMSMappingQuality RMSMappingQuality RMSMappingQuality UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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25 ReadPosRankSumTest ReadPosRankSumTest ReadPosRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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26 SampleList SampleList SampleList UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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27 SnpEff SnpEff SnpEff VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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28 SpanningDeletions SpanningDeletions SpanningDeletions UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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29 VariantType VariantType VariantType UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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30 AlleleCount Allele count in genotypes, for each ALT allele (AC) AC UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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31 AlleleFrequency Allele Frequency, for each ALT allele (AF) AF UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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32 AlleleNumber Total number of alleles in called genotypes (AN) AN UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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33 Coverage Unfiltered depth over all samples (DP) DP UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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34 Dels Dels Dels UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
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35 MQ RMS Mapping Quality MQ UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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36 MQ0 Mapping Quality Zero MQ0 UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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37 BaseQualityRankSumTest BaseQualityRankSumTest BaseQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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38 MappingQualityRankSumTest MappingQualityRankSumTest MappingQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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39 ReadPosRankSumTest ReadPosRankSumTest ReadPosRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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40 HaplotypeScore HaplotypeScore HaplotypeScore UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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41 QualByDepth QualByDepth QD UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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42 VQSLOD Variant quality score recalibration VQSLOD UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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43 FisherStrand FisherStrand FS UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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44 StrandBias Strand Bias evidence (higher SB, more bias, more false positive calls) SB UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
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