Commit 448cb3dd authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add QC plot for base recal

parent 3cd7b3bf
......@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
import nl.lumc.sasc.biopet.function._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk.{BaseRecalibrator, CommandLineGATK, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, GenotypeGVCFs}
import org.broadinstitute.sting.queue.extensions.gatk.{BaseRecalibrator, CommandLineGATK, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, GenotypeGVCFs, AnalyzeCovariates}
import org.broadinstitute.sting.queue.function._
import org.broadinstitute.sting.commandline._
import org.broadinstitute.sting.utils.variant.GATKVCFIndexType
......@@ -84,9 +84,25 @@ class GatkVariantcalling(val root:Configurable) extends QScript with BiopetQScri
if (configContains("scattercount", "baserecalibrator")) this.scatterCount = config("scattercount", 1, "baserecalibrator")
this.nct = config("threads", 2, "baserecalibrator")
}
baseRecalibrator.isIntermediate = true
add(baseRecalibrator)
val baseRecalibratorAfter = new BaseRecalibrator with gatkArguments {
this.I :+= inputBam
this.o = swapExt(dir,inputBam,".bam",".baserecal.after")
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")
}
add(baseRecalibratorAfter)
val analyzeCovariates = new AnalyzeCovariates with gatkArguments {
this.before = baseRecalibrator.o
this.after = baseRecalibratorAfter.o
this.plots = swapExt(dir,inputBam,".bam",".baserecal.pdf")
}
add(analyzeCovariates)
val printReads = new PrintReads with gatkArguments {
this.I :+= inputBam
this.o = swapExt(dir,inputBam,".bam",".baserecal.bam")
......
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