Convert more to biopet values
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- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala 4 additions, 4 deletions...sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala 11 additions, 59 deletions...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala 14 additions, 27 deletions...lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala 21 additions, 29 deletions...c/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala 22 additions, 66 deletions...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala 4 additions, 1 deletion...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
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