Commit ae952d4c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added min_mapping_quality_score to haplotypecaller

parent 62ed4c90
......@@ -36,6 +36,8 @@ class GatkVariantcalling(val root:Configurable) extends QScript with BiopetQScri
if (reference == null) reference = config("reference")
if (dbsnp == null && configContains("dbsnp")) dbsnp = config("dbsnp")
if (outputFile == null) outputFile = outputDir + outputName + (if (gvcfMode) ".gvcf.vcf" else ".vcf")
if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
else if (!outputDir.endsWith("/")) outputDir += "/"
}
def biopetScript() {
......@@ -82,7 +84,7 @@ class GatkVariantcalling(val root:Configurable) extends QScript with BiopetQScri
this.o = swapExt(dir,inputBam,".bam",".baserecal")
if (dbsnp != null) this.knownSites :+= dbsnp
if (configContains("scattercount", "baserecalibrator")) this.scatterCount = config("scattercount", 1, "baserecalibrator")
this.nct = config("threads", 2, "baserecalibrator")
this.nct = config("threads", 1, "baserecalibrator")
}
add(baseRecalibrator)
......@@ -92,7 +94,7 @@ class GatkVariantcalling(val root:Configurable) extends QScript with BiopetQScri
this.BQSR = baseRecalibrator.o
if (dbsnp != null) this.knownSites :+= dbsnp
if (configContains("scattercount", "baserecalibrator")) this.scatterCount = config("scattercount", 1, "baserecalibrator")
this.nct = config("threads", 2, "baserecalibrator")
this.nct = config("threads", 1, "baserecalibrator")
}
add(baseRecalibratorAfter)
......@@ -117,6 +119,7 @@ class GatkVariantcalling(val root:Configurable) extends QScript with BiopetQScri
def addHaplotypeCaller(bamfiles:List[File], outputfile:File): File = {
val haplotypeCaller = new HaplotypeCaller with gatkArguments {
this.min_mapping_quality_score = config("minMappingQualityScore", 20, "haplotypecaller")
if (configContains("scattercount", "haplotypecaller")) this.scatterCount = config("scattercount", 1, "haplotypecaller")
this.input_file = bamfiles
this.out = outputfile
......@@ -141,7 +144,7 @@ class GatkVariantcalling(val root:Configurable) extends QScript with BiopetQScri
this.dontUseSoftClippedBases = config("dontusesoftclippedbases", false, "haplotypecaller")
this.recoverDanglingHeads = config("recoverdanglingheads", false, "haplotypecaller")
this.stand_call_conf = config("stand_call_conf", 30, "haplotypecaller")
this.stand_emit_conf = config("stand_emit_conf", 10, "haplotypecaller")
this.stand_emit_conf = config("stand_emit_conf", 30, "haplotypecaller")
}
}
add(haplotypeCaller)
......@@ -156,6 +159,8 @@ class GatkVariantcalling(val root:Configurable) extends QScript with BiopetQScri
if (configContains("dbsnp")) this.dbsnp = config("dbsnp")
if (configContains("scattercount", "genotypegvcfs")) this.scatterCount = config("scattercount", 1, "genotypegvcfs")
this.out = outputDir + outputName + ".vcf"
this.stand_call_conf = config("stand_call_conf", 30, "genotypegvcfs")
this.stand_emit_conf = config("stand_emit_conf", 30, "genotypegvcfs")
}
add(genotypeGVCFs)
return genotypeGVCFs.out
......
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