Commit 5c545796 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added gvcf mode

parent f6841e2c
......@@ -2,6 +2,7 @@ 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.GenotypeGVCFs
import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcallingTrait
import org.broadinstitute.gatk.queue.QScript
......@@ -13,7 +14,8 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
def this() = this(null)
override def callers = {
new HaplotypeCallerAllele ::
new HaplotypeCallerGvcf ::
new HaplotypeCallerAllele ::
new UnifiedGenotyperAllele ::
new UnifiedGenotyper ::
new HaplotypeCaller ::
......@@ -69,7 +71,7 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
class UnifiedGenotyperAllele extends Variantcaller {
val name = "unifiedgenotyper_allele"
protected val defaultPrio = 6
protected val defaultPrio = 9
protected val defaultUse = false
def outputFile = new File(outputDir, namePrefix + "unifiedgenotyper_allele.vcf.gz")
......@@ -83,6 +85,28 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
add(ug)
}
}
class HaplotypeCallerGvcf extends Variantcaller {
val name = "haplotypecaller_gvcf"
protected val defaultPrio = 5
protected val defaultUse = false
def outputFile = new File(outputDir, namePrefix + "haplotypecaller_gvcf.vcf.gz")
def addJobs() {
val gvcfFiles = for (inputBam <- inputBams) yield {
val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(qscript)
hc.input_file = List(inputBam)
hc.out = new File(outputDir, inputBam.getName.stripSuffix(".bam") + ".gvcf.gz")
hc.useGvcf()
add(hc)
hc.out
}
val genotypeGVCFs = GenotypeGVCFs(qscript, gvcfFiles, outputFile)
add(genotypeGVCFs)
}
}
}
object ShivaVariantcallingGatk extends PipelineCommand
\ No newline at end of file
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