From c82692862600ddf4d74f797a15d1b0e7d090984a Mon Sep 17 00:00:00 2001 From: Peter van 't Hof <p.j.van_t_hof@lumc.nl> Date: Tue, 10 Jun 2014 17:45:26 +0200 Subject: [PATCH] SplitNCigarReads now before indel realign --- .../java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala index 6f42c1ac0..400ed4ad2 100644 --- a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala +++ b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala @@ -84,9 +84,10 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript mapping.script addAll(mapping.functions) // Add functions of mapping to curent function pool - var bamFile:File = addIndelRealign(mapping.outputFiles("finalBamFile"),runDir) // Indel realigner - bamFile = addBaseRecalibrator(bamFile,runDir) // Base recalibrator + var bamFile:File = mapping.outputFiles("finalBamFile") if (inputType == "rna") bamFile = addSplitNCigarReads(bamFile,runDir) + bamFile = addIndelRealign(bamFile,runDir) // Indel realigner + bamFile = addBaseRecalibrator(bamFile,runDir) // Base recalibrator outputFiles += ("FinalBam" -> bamFile) } else this.logger.error("Sample: " + sampleID + ": No R1 found for run: " + runConfig) @@ -159,7 +160,8 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount") this.input_file = Seq(inputBam) this.out = swapExt(dir,inputBam,".bam",".split.bam") - this.read_filter :+= "ReassignMappingQuality -DMQ 60" + this.read_filter :+= "ReassignMappingQuality" + this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.ALLOW_N_CIGAR_READS } add(splitNCigarReads) -- GitLab