From 06a147a3b979a4f7b2310da84a136207a1d528b4 Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Thu, 6 Apr 2017 16:10:43 +0200 Subject: [PATCH] Adding bqsr implementation --- .../shiva/variantcallers/HaplotypeCallerAllele.scala | 9 ++++++++- .../shiva/variantcallers/UnifiedGenotyperAllele.scala | 8 ++++++++ 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala index e36f4c758..a2ded8a46 100644 --- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala +++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala @@ -20,7 +20,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers import nl.lumc.sasc.biopet.extensions.gatk -import nl.lumc.sasc.biopet.utils.Logging +import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather import nl.lumc.sasc.biopet.utils.config.Configurable /** Allele mode for Haplotypecaller */ @@ -33,6 +33,13 @@ class HaplotypeCallerAllele(val parent: Configurable) extends Variantcaller { def biopetScript() { val hc = gatk.HaplotypeCaller(this, inputBams.values.toList, outputFile) hc.alleles = Some(alleles) + hc.BQSR = if (inputBqsrFiles.isEmpty) None else { + val gather = new BqsrGather + gather.inputBqsrFiles = inputBqsrFiles.values.toList + gather.outputBqsrFile = new File(outputDir, "bqsr.merge") + add(gather) + Some(gather.outputBqsrFile) + } hc.genotyping_mode = Some("GENOTYPE_GIVEN_ALLELES") add(hc) } diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala index 4d2b9501e..61fc86c6b 100644 --- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala +++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala @@ -20,6 +20,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers import nl.lumc.sasc.biopet.extensions.gatk +import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather import nl.lumc.sasc.biopet.utils.config.Configurable /** Allele mode for GenotyperAllele */ @@ -33,6 +34,13 @@ class UnifiedGenotyperAllele(val parent: Configurable) extends Variantcaller { val ug = gatk.UnifiedGenotyper(this, inputBams.values.toList, outputFile) ug.alleles = Some(alleles) ug.genotyping_mode = Some("GENOTYPE_GIVEN_ALLELES") + ug.BQSR = if (inputBqsrFiles.isEmpty) None else { + val gather = new BqsrGather + gather.inputBqsrFiles = inputBqsrFiles.values.toList + gather.outputBqsrFile = new File(outputDir, "bqsr.merge") + add(gather) + Some(gather.outputBqsrFile) + } add(ug) } } -- GitLab