From 9e565c2f346f96305147634d55ff8f7f051bc71f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 17 Nov 2014 08:54:45 +0100
Subject: [PATCH] Added useIndelRealigner and useBaseRecalibration option
---
.../pipelines/gatk/GatkVariantcalling.scala | 27 ++++++++++++++-----
1 file changed, 20 insertions(+), 7 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 b016e17dc..915371c72 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
@@ -41,12 +41,20 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
var useHaplotypecaller: Option[Boolean] = config("use_haplotypecaller", default = true)
var useUnifiedGenotyper: Option[Boolean] = config("use_unifiedgenotyper", default = false)
var useAllelesOption: Option[Boolean] = config("use_alleles_option", default = false)
+ var useIndelRealigner: Boolean = config("use_indel_realign", default = true)
+ var useBaseRecalibration: Boolean = config("use_base_recalibration", default = true)
def init() {
if (outputName == null && sampleID != null) outputName = sampleID
else if (outputName == null) outputName = "noname"
if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
else if (!outputDir.endsWith("/")) outputDir += "/"
+
+ val baseRecalibrator = new BaseRecalibrator(this)
+ if (useBaseRecalibration && baseRecalibrator.knownSites.isEmpty) {
+ logger.warn("No Known site found, skipping base recalibration")
+ useBaseRecalibration = false
+ }
}
private def doublePreProces(files: List[File]): List[File] = {
@@ -54,11 +62,10 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
if (files.isEmpty) throw new IllegalStateException("Files can't be empty")
if (!doublePreProces.get) return files
val markDub = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
- if (dbsnp != null) {
- add(markDub, isIntermediate = true)
+ add(markDub, isIntermediate = useIndelRealigner)
+ if (useIndelRealigner) {
List(addIndelRealign(markDub.output, outputDir, isIntermediate = false))
} else {
- add(markDub, isIntermediate = true)
List(markDub.output)
}
}
@@ -67,8 +74,14 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
scriptOutput.bamFiles = if (preProcesBams.get) {
var bamFiles: List[File] = Nil
for (inputBam <- inputBams) {
- var bamFile = addIndelRealign(inputBam, outputDir)
- bamFiles :+= addBaseRecalibrator(bamFile, outputDir, isIntermediate = bamFiles.size > 1)
+ var bamFile = inputBam
+ if (useIndelRealigner) {
+ bamFile = addIndelRealign(bamFile, outputDir, isIntermediate = useBaseRecalibration)
+ }
+ if (useBaseRecalibration) {
+ bamFile = addBaseRecalibrator(bamFile, outputDir, isIntermediate = bamFiles.size > 1)
+ }
+ bamFiles :+= bamFile
}
doublePreProces(bamFiles)
} else if (inputBams.size > 1 && doublePreProces.get) {
@@ -188,7 +201,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
}
def addBaseRecalibrator(inputBam: File, dir: String, isIntermediate: Boolean = false): File = {
- val baseRecalibrator = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal")) //with gatkArguments {
+ val baseRecalibrator = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal"))
if (baseRecalibrator.knownSites.isEmpty) {
logger.warn("No Known site found, skipping base recalibration, file: " + inputBam)
@@ -196,7 +209,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
}
add(baseRecalibrator)
- val baseRecalibratorAfter = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.after")) //with gatkArguments {
+ val baseRecalibratorAfter = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.after"))
baseRecalibratorAfter.BQSR = baseRecalibrator.o
add(baseRecalibratorAfter)
--
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