Merge branch 'fix-Shiva_bcftools_calling' into 'develop'
Fix shiva bcftools calling - [x] Test bcftools - [x] Add merge to bcftools singlesample - [x] Test bcftools singlesample See merge request !254
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- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala 1 addition, 1 deletion...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
- protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala 7 additions, 3 deletions.../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala 2 additions, 2 deletions...scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala 21 additions, 5 deletions...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala 2 additions, 0 deletions...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala 47 additions, 9 deletions...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala 49 additions, 0 deletions.../lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala 2 additions, 0 deletions...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala 4 additions, 7 deletions...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala 1 addition, 1 deletion...l/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala 9 additions, 20 deletions...a/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
- public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala 2 additions, 2 deletions...c/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala 4 additions, 4 deletions...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala 50 additions, 15 deletions...asc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
- public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala 15 additions, 4 deletions...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
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