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)
--
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