# HG changeset patch # User sanbi-uwc # Date 1524210137 14400 # Node ID 5805746de7f08df1444247b775daba3f5d7bb55c # Parent 3f355d234d6fb8ab81649809dc59499b33eadf97 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit 51cb0f5195eaa6961fedbdd0e7d12720936a1ecd diff -r 3f355d234d6f -r 5805746de7f0 gatk2_annotations.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gatk2_annotations.loc.sample Fri Apr 20 03:42:17 2018 -0400 @@ -0,0 +1,26 @@ +#unique_id name gatk_value tools_valid_for +AlleleBalance AlleleBalance AlleleBalance UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +AlleleBalanceBySample AlleleBalanceBySample AlleleBalanceBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +BaseCounts BaseCounts BaseCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +BaseQualityRankSumTest BaseQualityRankSumTest BaseQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +ChromosomeCounts ChromosomeCounts ChromosomeCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +Coverage Coverage Coverage UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +DepthPerAlleleBySample DepthPerAlleleBySample DepthPerAlleleBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +FisherStrand FisherStrand FisherStrand UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +GCContent GCContent GCContent UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +HaplotypeScore HaplotypeScore HaplotypeScore UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +HardyWeinberg HardyWeinberg HardyWeinberg UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +HomopolymerRun HomopolymerRun HomopolymerRun UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +InbreedingCoeff InbreedingCoeff InbreedingCoeff UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +LowMQ LowMQ LowMQ UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +MVLikelihoodRatio MVLikelihoodRatio MVLikelihoodRatio VariantAnnotator,VariantRecalibrator,HaplotypeCaller +MappingQualityRankSumTest MappingQualityRankSumTest MappingQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +MappingQualityZero MappingQualityZero MappingQualityZero UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +MappingQualityZeroBySample MappingQualityZeroBySample MappingQualityZeroBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +NBaseCount NBaseCount NBaseCount UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +QualByDepth QualByDepth QualByDepth UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +RMSMappingQuality RMSMappingQuality RMSMappingQuality UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +ReadPosRankSumTest ReadPosRankSumTest ReadPosRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +SampleList SampleList SampleList UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +SnpEff SnpEff SnpEff VariantAnnotator,VariantRecalibrator,HaplotypeCaller +SpanningDeletions SpanningDeletions SpanningDeletions UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller diff -r 3f355d234d6f -r 5805746de7f0 gatk2_annotations.txt.sample --- a/gatk2_annotations.txt.sample Fri Apr 20 03:37:00 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -#unique_id name gatk_value tools_valid_for -AlleleBalance AlleleBalance AlleleBalance UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -AlleleBalanceBySample AlleleBalanceBySample AlleleBalanceBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -BaseCounts BaseCounts BaseCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -BaseQualityRankSumTest BaseQualityRankSumTest BaseQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -ChromosomeCounts ChromosomeCounts ChromosomeCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -Coverage Coverage Coverage UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -DepthPerAlleleBySample DepthPerAlleleBySample DepthPerAlleleBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -FisherStrand FisherStrand FisherStrand UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -GCContent GCContent GCContent UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -HaplotypeScore HaplotypeScore HaplotypeScore UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -HardyWeinberg HardyWeinberg HardyWeinberg UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -HomopolymerRun HomopolymerRun HomopolymerRun UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -InbreedingCoeff InbreedingCoeff InbreedingCoeff UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -LowMQ LowMQ LowMQ UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -MVLikelihoodRatio MVLikelihoodRatio MVLikelihoodRatio VariantAnnotator,VariantRecalibrator,HaplotypeCaller -MappingQualityRankSumTest MappingQualityRankSumTest MappingQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -MappingQualityZero MappingQualityZero MappingQualityZero UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -MappingQualityZeroBySample MappingQualityZeroBySample MappingQualityZeroBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -NBaseCount NBaseCount NBaseCount UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -QualByDepth QualByDepth QualByDepth UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -RMSMappingQuality RMSMappingQuality RMSMappingQuality UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -ReadPosRankSumTest ReadPosRankSumTest ReadPosRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -SampleList SampleList SampleList UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -SnpEff SnpEff SnpEff VariantAnnotator,VariantRecalibrator,HaplotypeCaller -SpanningDeletions SpanningDeletions SpanningDeletions UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller diff -r 3f355d234d6f -r 5805746de7f0 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Fri Apr 20 03:37:00 2018 -0400 +++ b/tool_data_table_conf.xml.sample Fri Apr 20 03:42:17 2018 -0400 @@ -7,6 +7,6 @@ value, name, gatk_value, tools_valid_for - +