Mercurial > repos > sanbi-uwc > gatk2
changeset 4:5805746de7f0 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit 51cb0f5195eaa6961fedbdd0e7d12720936a1ecd
| author | sanbi-uwc |
|---|---|
| date | Fri, 20 Apr 2018 03:42:17 -0400 |
| parents | 3f355d234d6f |
| children | 6e5c52be3502 |
| files | gatk2_annotations.loc.sample gatk2_annotations.txt.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 27 insertions(+), 27 deletions(-) [+] |
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--- /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
--- 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
--- 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 @@ <!-- Available of GATK references --> <table name="gatk2_annotations" comment_char="#"> <columns>value, name, gatk_value, tools_valid_for</columns> - <file path="tool-data/gatk2_annotations.loc.sample" /> + <file path="tool-data/gatk2_annotations.loc" /> </table> </tables>