diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala index b29c9efb7c570251dbe762b3a434a441f73640f1..9bc68f233704500e3863f5c7bc41e45149c9e26c 100644 --- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala +++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala @@ -168,7 +168,9 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag { /** Makes a vcf file from a mpileup without statistics */ class RawVcf extends Variantcaller { val name = "raw" - protected val defaultPrio = 999 + + // This caller is designed as fallback when other variantcallers fails to report + protected val defaultPrio = Int.MaxValue /** Final output file of this mode */ def outputFile = new File(outputDir, namePrefix + ".raw.vcf.gz")