Commit c8269286 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

SplitNCigarReads now before indel realign

parent 29bf997a
...@@ -84,9 +84,10 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript ...@@ -84,9 +84,10 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript
mapping.script mapping.script
addAll(mapping.functions) // Add functions of mapping to curent function pool addAll(mapping.functions) // Add functions of mapping to curent function pool
var bamFile:File = addIndelRealign(mapping.outputFiles("finalBamFile"),runDir) // Indel realigner var bamFile:File = mapping.outputFiles("finalBamFile")
bamFile = addBaseRecalibrator(bamFile,runDir) // Base recalibrator
if (inputType == "rna") bamFile = addSplitNCigarReads(bamFile,runDir) if (inputType == "rna") bamFile = addSplitNCigarReads(bamFile,runDir)
bamFile = addIndelRealign(bamFile,runDir) // Indel realigner
bamFile = addBaseRecalibrator(bamFile,runDir) // Base recalibrator
outputFiles += ("FinalBam" -> bamFile) outputFiles += ("FinalBam" -> bamFile)
} else this.logger.error("Sample: " + sampleID + ": No R1 found for run: " + runConfig) } 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 ...@@ -159,7 +160,8 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript
if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount") if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
this.input_file = Seq(inputBam) this.input_file = Seq(inputBam)
this.out = swapExt(dir,inputBam,".bam",".split.bam") 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 this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.ALLOW_N_CIGAR_READS
} }
add(splitNCigarReads) add(splitNCigarReads)
......
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