Commit 25ee758d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding UnifiedGenotyper

parent 3c2bd820
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.broad._
import nl.lumc.sasc.biopet.pipelines.shiva.{ShivaVariantcallingTrait, ShivaVariantcalling, ShivaTrait}
import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaVariantcallingTrait, ShivaVariantcalling, ShivaTrait }
import org.broadinstitute.gatk.queue.QScript
/**
......
......@@ -2,7 +2,6 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller
import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcallingTrait
import org.broadinstitute.gatk.queue.QScript
......@@ -13,9 +12,9 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
qscript =>
def this() = this(null)
override def callers = new Haplotypecaller :: super.callers
override def callers = new UnifiedGenotyper :: new HaplotypeCaller :: super.callers
class Haplotypecaller extends Variantcaller {
class HaplotypeCaller extends Variantcaller {
val name = "haplotypecaller"
protected val defaultPrio = 1
protected val defaultUse = true
......@@ -23,7 +22,22 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
def outputFile = new File(outputDir, namePrefix + "haplotypecaller.vcf.gz")
def addJobs() {
val hc = new HaplotypeCaller(qscript)
val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(qscript)
hc.input_file = inputBams
hc.out = outputFile
add(hc)
}
}
class UnifiedGenotyper extends Variantcaller {
val name = "unifiedgenotyper"
protected val defaultPrio = 20
protected val defaultUse = false
def outputFile = new File(outputDir, namePrefix + "unifiedgenotyper.vcf.gz")
def addJobs() {
val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.UnifiedGenotyper(qscript)
hc.input_file = inputBams
hc.out = outputFile
add(hc)
......
......@@ -23,8 +23,8 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
def namePrefix: String = {
(sampleId, libId) match {
case (Some(sampleId), Some(libId)) => sampleId + "-" + libId + "."
case (Some(sampleId), _) => sampleId + "."
case _ => ""
case (Some(sampleId), _) => sampleId + "."
case _ => ""
}
}
......
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