Commit 7313c86d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change to mergeAlleles

parent 61128d4e
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import java.io.File
import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter }
import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter , MergeAlleles}
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.{ AnalyzeCovariates, BaseRecalibrator, GenotypeGVCFs, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, SelectVariants, CombineVariants, UnifiedGenotyper }
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
......@@ -135,26 +135,14 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
mergBuffer += ("9.raw" -> scriptOutput.rawFilterVcfFile)
if (useAllelesOption.get) {
val tempFile = if (mergeList.toList.size > 1) {
val allelesTemp = CombineVariants(this, mergeList.toList, outputDir + outputName + ".alleles_temp.vcf.gz")
allelesTemp.genotypemergeoption = org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.GenotypeMergeType.UNSORTED
add(allelesTemp, isIntermediate = true)
allelesTemp.out
} else mergeList.toList.head
val alleleOnly = new CommandLineFunction {
@Input val input: File = tempFile
@Output val output: File = outputDir + "raw.allele_only.vcf.gz"
@Output val outputindex: File = outputDir + "raw.allele__temp_only.vcf.gz.tbi"
def commandLine = "zcat " + input + " | cut -f1,2,3,4,5,6,7,8 | bgzip -c > " + output + " && tabix -pvcf " + output
}
add(alleleOnly, isIntermediate = true)
val mergeAlleles = MergeAlleles(this,mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz.tbi")
add(mergeAlleles, isIntermediate = true)
if (useHaplotypecaller.get) {
val hcAlleles = new HaplotypeCaller(this)
hcAlleles.input_file = scriptOutput.bamFiles
hcAlleles.out = outputDir + outputName + ".hc.allele.vcf.gz"
hcAlleles.alleles = alleleOnly.output
hcAlleles.alleles = mergeAlleles.output
hcAlleles.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
add(hcAlleles)
scriptOutput.hcAlleleVcf = hcAlleles.out
......@@ -165,7 +153,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
val ugAlleles = new UnifiedGenotyper(this)
ugAlleles.input_file = scriptOutput.bamFiles
ugAlleles.out = outputDir + outputName + ".ug.allele.vcf.gz"
ugAlleles.alleles = alleleOnly.output
ugAlleles.alleles = mergeAlleles.output
ugAlleles.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
add(ugAlleles)
scriptOutput.ugAlleleVcf = ugAlleles.out
......
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