From 7313c86dfba0adf793ad2ada1ead735da79864d1 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 8 Nov 2014 18:57:06 +0100
Subject: [PATCH] Change to mergeAlleles
---
.../pipelines/gatk/GatkVariantcalling.scala | 22 +++++--------------
1 file changed, 5 insertions(+), 17 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 23e6c81b6..572a3a276 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -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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