From 5121ff2084f96371a1682a4e79ecb0064742b89e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 4 Feb 2015 18:51:45 +0100
Subject: [PATCH] Added vcfstats to gatk pipeline
---
.../biopet/pipelines/gatk/GatkVariantcalling.scala | 8 +++++++-
.../scala/nl/lumc/sasc/biopet/tools/VcfStats.scala | 11 +++++++++--
2 files changed, 16 insertions(+), 3 deletions(-)
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 230eff772..10036b6bc 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -7,7 +7,7 @@ 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, MergeAlleles }
+import nl.lumc.sasc.biopet.tools.{ VcfStats, 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
@@ -197,6 +197,12 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
val cvFinal = CombineVariants(this, mergeList.toList, outputDir + outputName + ".final.vcf.gz")
cvFinal.genotypemergeoption = org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.GenotypeMergeType.UNSORTED
add(cvFinal)
+
+ val vcfStats = new VcfStats(this)
+ vcfStats.input = cvFinal.out
+ vcfStats.setOutputDir(outputDir + File.separator + "vcfstats")
+ add(vcfStats)
+
scriptOutput.finalVcfFile = cvFinal.out
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
index df32ef92d..d2ba5a337 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
@@ -22,7 +22,14 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction {
var input: File = _
@Output(doc = "Output fastq", shortName = "o", required = true)
- var output: File = _
+ protected var generalTsv: File = _
+
+ protected var outputDir: String = _
+
+ def setOutputDir(dir: String): Unit = {
+ outputDir = dir
+ generalTsv = new File(dir + File.separator + "genotype_general.tsv")
+ }
/**
* Creates command to execute extension
@@ -30,7 +37,7 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction {
*/
override def commandLine = super.commandLine +
required("-I", input) +
- required("-o", output)
+ required("-o", outputDir)
}
object VcfStats extends ToolCommand {
--
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