From 7e7762a9f374ab90f1ad2de17b930510ebeb5494 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 Jun 2014 09:42:28 +0200
Subject: [PATCH] getThreads function implemented in gatk functions
---
.../sasc/biopet/pipelines/gatk/Gatk.scala | 116 ++++++++++--------
1 file changed, 64 insertions(+), 52 deletions(-)
diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
index e23a0ec14..9a26bf9d5 100644
--- a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
+++ b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
@@ -133,7 +133,7 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript
this.o = swapExt(dir,inputBam,".bam",".baserecal")
this.knownSites :+= dbsnp
if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
- this.nct = 2
+ this.nct = this.config.getThreads(2)
}
add(baseRecalibrator)
@@ -156,7 +156,7 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript
this.input_file = bamfiles
this.out = outputfile
if (dbsnp != null) this.dbsnp = qscript.dbsnp
- this.nct = 3
+ this.nct = this.config.getThreads(3)
this.memoryLimit = this.nct * 2
// GVCF options
@@ -170,71 +170,83 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript
}
def addSnpVariantRecalibrator(inputVcf:File, dir:String): File = {
- val snpVariantRecalibrator = new VariantRecalibrator() with gatkArguments {
- val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("variantrecalibrator"), qscript.config)
- this.input +:= inputVcf
- this.nt = 4
- this.memoryLimit = 2 * nt
- this.recal_file = swapExt(dir, inputVcf,".vcf",".snp.recal")
- this.tranches_file = swapExt(dir, inputVcf,".vcf",".snp.tranches")
- this.resource = Seq(new TaggedFile(config.getAsString("hapmap"), "known=false,training=true,truth=true,prior=15.0"),
- new TaggedFile(config.getAsString("omni"), "known=false,training=true,truth=true,prior=12.0"),
- new TaggedFile(config.getAsString("1000G"), "known=false,training=true,truth=false,prior=10.0"),
- new TaggedFile(config.getAsString("dbsnp"), "known=true,training=false,truth=false,prior=2.0"))
- this.an = Seq("QD","MQ","MQRankSum","ReadPosRankSum","FS","DP","InbreedingCoeff")
- this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
- }
+ val snpVariantRecalibrator = getVariantRecalibrator("snp")
+ snpVariantRecalibrator.input +:= inputVcf
+ snpVariantRecalibrator.recal_file = swapExt(dir, inputVcf,".vcf",".snp.recal")
+ snpVariantRecalibrator.tranches_file = swapExt(dir, inputVcf,".vcf",".snp.tranches")
add(snpVariantRecalibrator)
- val snpApplyRecalibration = new ApplyRecalibration() with gatkArguments {
- val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("applyrecalibration"), qscript.config)
- this.input +:= inputVcf
- this.recal_file = snpVariantRecalibrator.recal_file
- this.tranches_file = snpVariantRecalibrator.tranches_file
- this.out = swapExt(dir, inputVcf,".vcf",".snp.recal.vcf")
- this.ts_filter_level = 99.5
- this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
- this.nt = 3
- this.memoryLimit = 2 * nt
- if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
- }
+ val snpApplyRecalibration = getApplyRecalibration("snp")
+ snpApplyRecalibration.input +:= inputVcf
+ snpApplyRecalibration.recal_file = snpVariantRecalibrator.recal_file
+ snpApplyRecalibration.tranches_file = snpVariantRecalibrator.tranches_file
+ snpApplyRecalibration.out = swapExt(dir, inputVcf,".vcf",".snp.recal.vcf")
add(snpApplyRecalibration)
return snpApplyRecalibration.out
}
def addIndelVariantRecalibrator(inputVcf:File, dir:String): File = {
- val indelVariantRecalibrator = new VariantRecalibrator() with gatkArguments {
- val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("variantrecalibrator"), qscript.config)
- this.input +:= inputVcf
- this.nt = 4
- this.memoryLimit = 2 * nt
- this.recal_file = swapExt(dir, inputVcf,".vcf",".indel.recal")
- this.tranches_file = swapExt(dir, inputVcf,".vcf",".indel.tranches")
- this.resource :+= new TaggedFile(config.getAsString("mills"), "known=false,training=true,truth=true,prior=12.0")
- this.resource :+= new TaggedFile(config.getAsString("dbsnp"), "known=true,training=false,truth=false,prior=2.0")
- this.an = Seq("QD","DP","FS","ReadPosRankSum","MQRankSum")
- this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
- }
+ val indelVariantRecalibrator = getVariantRecalibrator("indel")
+ indelVariantRecalibrator.input +:= inputVcf
+ indelVariantRecalibrator.recal_file = swapExt(dir, inputVcf,".vcf",".indel.recal")
+ indelVariantRecalibrator.tranches_file = swapExt(dir, inputVcf,".vcf",".indel.tranches")
add(indelVariantRecalibrator)
- val indelApplyRecalibration = new ApplyRecalibration() with gatkArguments {
- val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("applyrecalibration"), qscript.config)
- this.input +:= inputVcf
- this.recal_file = indelVariantRecalibrator.recal_file
- this.tranches_file = indelVariantRecalibrator.tranches_file
- this.out = swapExt(dir, inputVcf,".vcf",".indel.recal.vcf")
- this.ts_filter_level = 99.0
- this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
- this.nt = 3
- this.memoryLimit = 2 * nt
- if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
- }
+ val indelApplyRecalibration = getApplyRecalibration("indel")
+ indelApplyRecalibration.input +:= inputVcf
+ indelApplyRecalibration.recal_file = indelVariantRecalibrator.recal_file
+ indelApplyRecalibration.tranches_file = indelVariantRecalibrator.tranches_file
+ indelApplyRecalibration.out = swapExt(dir, inputVcf,".vcf",".indel.recal.vcf")
add(indelApplyRecalibration)
return indelApplyRecalibration.out
}
+ def getVariantRecalibrator(mode_arg:String) : VariantRecalibrator = {
+ val variantRecalibrator = new VariantRecalibrator() with gatkArguments {
+ var config = Config.mergeConfigs(qscript.config.getAsConfig("variantrecalibrator"), qscript.config)
+ if (mode_arg == "indel") {
+ this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
+ this.config = Config.mergeConfigs(this.config.getAsConfig("indel"),this.config)
+ if (config.contains("mills")) this.resource :+= new TaggedFile(this.config.getAsString("mills"), "known=false,training=true,truth=true,prior=12.0")
+ } else { // SNP
+ this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
+ this.config = Config.mergeConfigs(this.config.getAsConfig("snp"),this.config)
+ if (this.config.contains("hapmap")) this.resource +:= new TaggedFile(this.config.getAsString("hapmap"), "known=false,training=true,truth=true,prior=15.0")
+ if (this.config.contains("omni")) this.resource +:= new TaggedFile(this.config.getAsString("omni"), "known=false,training=true,truth=true,prior=12.0")
+ if (this.config.contains("1000G")) this.resource +:= new TaggedFile(this.config.getAsString("1000G"), "known=false,training=true,truth=false,prior=10.0")
+ }
+ logger.debug("VariantRecalibrator-" + mode_arg + ": " + this.config)
+ if (this.config.contains("dbsnp")) this.resource :+= new TaggedFile(this.config.getAsString("dbsnp"), "known=true,training=false,truth=false,prior=2.0")
+ this.nt = config.getThreads(4)
+ this.memoryLimit = 2 * nt
+ this.an = Seq("QD","DP","FS","ReadPosRankSum","MQRankSum")
+ if (this.config.contains("minnumbadvariants")) this.minNumBadVariants = this.config.getAsInt("minnumbadvariants")
+ if (this.config.contains("maxgaussians")) this.maxGaussians = this.config.getAsInt("maxgaussians")
+ }
+ return variantRecalibrator
+ }
+
+ def getApplyRecalibration(mode_arg:String) : ApplyRecalibration = {
+ val applyRecalibration = new ApplyRecalibration() with gatkArguments {
+ var config = Config.mergeConfigs(qscript.config.getAsConfig("applyrecalibration"), qscript.config)
+ if (mode_arg == "indel") {
+ this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
+ this.config = Config.mergeConfigs(this.config.getAsConfig("indel"),this.config)
+ this.ts_filter_level = this.config.getAsDouble("ts_filter_level", 99.0)
+ } else { // SNP
+ this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
+ this.config = Config.mergeConfigs(this.config.getAsConfig("snp"),this.config)
+ this.ts_filter_level = this.config.getAsDouble("ts_filter_level", 99.5)
+ }
+ this.nt = config.getThreads(3)
+ this.memoryLimit = 2 * nt
+ if (config.contains("scattercount")) this.scatterCount = this.config.getAsInt("scattercount")
+ }
+ return applyRecalibration
+ }
+
def addGenotypeGVCFs(gvcfFiles: List[File], dir:String): File = {
val genotypeGVCFs = new GenotypeGVCFs() with gatkArguments {
val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("genotypegvcfs"), qscript.config)
--
GitLab