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Commit 3f2913f8 authored by Peter van 't Hof's avatar Peter van 't Hof
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- Fixed memory issue in Variant Recalibration

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gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
+ 47
− 42
View file @ 3f2913f8
......@@ -60,58 +60,63 @@ class Gatk(private var globalConfig: Config) extends QScript {
add(genotypeGVCFs)
//Snp recal
val snpVariantRecalibrator = new VariantRecalibrator() with gatkArguments
snpVariantRecalibrator.input +:= genotypeGVCFs.out
snpVariantRecalibrator.nt = 8
snpVariantRecalibrator.recal_file = swapExt(genotypeGVCFs.out,".vcf",".snp.recal")
snpVariantRecalibrator.tranches_file = swapExt(genotypeGVCFs.out,".vcf",".snp.tranches")
snpVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("hapmap"), "known=false,training=true,truth=true,prior=15.0")
snpVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("omni"), "known=false,training=true,truth=true,prior=12.0")
snpVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("1000G"), "known=false,training=true,truth=false,prior=10.0")
snpVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("dbsnp"), "known=true,training=false,truth=false,prior=2.0")
snpVariantRecalibrator.an = Seq("QD","MQ","MQRankSum","ReadPosRankSum","FS","DP","InbreedingCoeff")
snpVariantRecalibrator.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
val snpVariantRecalibrator = new VariantRecalibrator() with gatkArguments {
input +:= genotypeGVCFs.out
nt = 4; memoryLimit = 2 * nt
recal_file = swapExt(genotypeGVCFs.out,".vcf",".snp.recal")
tranches_file = swapExt(genotypeGVCFs.out,".vcf",".snp.tranches")
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"))
an = Seq("QD","MQ","MQRankSum","ReadPosRankSum","FS","DP","InbreedingCoeff")
mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
}
add(snpVariantRecalibrator)
val snpApplyRecalibration = new ApplyRecalibration() with gatkArguments
snpApplyRecalibration.input +:= genotypeGVCFs.out
snpApplyRecalibration.recal_file = snpVariantRecalibrator.recal_file
snpApplyRecalibration.tranches_file = snpVariantRecalibrator.tranches_file
snpApplyRecalibration.out = swapExt(genotypeGVCFs.out,".vcf",".snp.recal.vcf")
snpApplyRecalibration.ts_filter_level = 99.5
snpApplyRecalibration.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
snpApplyRecalibration.nt = 3
snpApplyRecalibration.scatterCount = scatterCount
val snpApplyRecalibration = new ApplyRecalibration() with gatkArguments {
input +:= genotypeGVCFs.out
recal_file = snpVariantRecalibrator.recal_file
tranches_file = snpVariantRecalibrator.tranches_file
out = swapExt(genotypeGVCFs.out,".vcf",".snp.recal.vcf")
ts_filter_level = 99.5
mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
nt = 3; memoryLimit = 2 * nt
scatterCount = scatterCount
}
add(snpApplyRecalibration)
//indel recal
val indelVariantRecalibrator = new VariantRecalibrator() with gatkArguments
indelVariantRecalibrator.input +:= genotypeGVCFs.out
indelVariantRecalibrator.nt = 8
indelVariantRecalibrator.recal_file = swapExt(genotypeGVCFs.out,".vcf",".indel.recal")
indelVariantRecalibrator.tranches_file = swapExt(genotypeGVCFs.out,".vcf",".indel.tranches")
indelVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("mills"), "known=false,training=true,truth=true,prior=12.0")
indelVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("dbsnp"), "known=true,training=false,truth=false,prior=2.0")
indelVariantRecalibrator.an = Seq("QD","DP","FS","ReadPosRankSum","MQRankSum","InbreedingCoeff")
indelVariantRecalibrator.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
val indelVariantRecalibrator = new VariantRecalibrator() with gatkArguments {
input +:= genotypeGVCFs.out
nt = 4; memoryLimit = 2 * nt
recal_file = swapExt(genotypeGVCFs.out,".vcf",".indel.recal")
tranches_file = swapExt(genotypeGVCFs.out,".vcf",".indel.tranches")
resource :+= new TaggedFile(config.getAsString("mills"), "known=false,training=true,truth=true,prior=12.0")
resource :+= new TaggedFile(config.getAsString("dbsnp"), "known=true,training=false,truth=false,prior=2.0")
an = Seq("QD","DP","FS","ReadPosRankSum","MQRankSum","InbreedingCoeff")
mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
}
add(indelVariantRecalibrator)
val indelApplyRecalibration = new ApplyRecalibration() with gatkArguments
indelApplyRecalibration.input +:= genotypeGVCFs.out
indelApplyRecalibration.recal_file = indelVariantRecalibrator.recal_file
indelApplyRecalibration.tranches_file = indelVariantRecalibrator.tranches_file
indelApplyRecalibration.out = swapExt(genotypeGVCFs.out,".vcf",".indel.recal.vcf")
indelApplyRecalibration.ts_filter_level = 99.0
indelApplyRecalibration.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
indelApplyRecalibration.nt = 3
indelApplyRecalibration.scatterCount = scatterCount
val indelApplyRecalibration = new ApplyRecalibration() with gatkArguments {
input +:= genotypeGVCFs.out
recal_file = indelVariantRecalibrator.recal_file
tranches_file = indelVariantRecalibrator.tranches_file
out = swapExt(genotypeGVCFs.out,".vcf",".indel.recal.vcf")
ts_filter_level = 99.0
mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
nt = 3; memoryLimit = 2 * nt
scatterCount = scatterCount
}
add(indelApplyRecalibration)
// merge snp and indels
val catVariants = new CatVariants()
catVariants.variant = Seq(snpApplyRecalibration.out,indelApplyRecalibration.out)
catVariants.outputFile = swapExt(genotypeGVCFs.out,".vcf",".recal.vcf")
catVariants.reference = referenceFile
val catVariants = new CatVariants() {
variant = Seq(snpApplyRecalibration.out,indelApplyRecalibration.out)
outputFile = swapExt(genotypeGVCFs.out,".vcf",".recal.vcf")
reference = referenceFile
}
add(catVariants)
} else logger.warn("No gVCFs to genotype")
......
mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+ 32
− 31
View file @ 3f2913f8
......@@ -80,7 +80,6 @@ class Mapping(private var globalConfig: Config) extends QScript {
if (paired) fastq_R2 = flexiprep.outputFiles("output_R2")
}
var bamFile:File = ""
//var samFile:File = ""
if (aligner == "bwa") {
val bwaCommand = new Bwa(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2;
RG = getReadGroup; output = new File(outputDir + outputName + ".sam") }
......@@ -96,46 +95,48 @@ class Mapping(private var globalConfig: Config) extends QScript {
}
def addSortSam(inputSam:List[File], outputFile:File, dir:String) : File = {
val sortSam = new SortSam
sortSam.input = inputSam
sortSam.createIndex = true
sortSam.output = outputFile
sortSam.memoryLimit = 2
sortSam.nCoresRequest = 2
sortSam.jobResourceRequests :+= "h_vmem=4G"
val sortSam = new SortSam {
input = inputSam
createIndex = true
output = outputFile
memoryLimit = 2
nCoresRequest = 2
jobResourceRequests :+= "h_vmem=4G"
}
add(sortSam)
return sortSam.output
}
def addAddOrReplaceReadGroups(inputSam:List[File], outputFile:File, dir:String) : File = {
val addOrReplaceReadGroups = new AddOrReplaceReadGroups
addOrReplaceReadGroups.input = inputSam
addOrReplaceReadGroups.createIndex = true
addOrReplaceReadGroups.output = outputFile
addOrReplaceReadGroups.memoryLimit = 2
addOrReplaceReadGroups.nCoresRequest = 2
addOrReplaceReadGroups.jobResourceRequests :+= "h_vmem=4G"
addOrReplaceReadGroups.RGLB = RGLB
addOrReplaceReadGroups.RGPL = RGPL
addOrReplaceReadGroups.RGPU = RGPU
addOrReplaceReadGroups.RGSM = RGSM
if (RGCN != null) addOrReplaceReadGroups.RGCN = RGCN
if (RGDS != null) addOrReplaceReadGroups.RGDS = RGDS
val addOrReplaceReadGroups = new AddOrReplaceReadGroups {
input = inputSam
output = outputFile
createIndex = true
memoryLimit = 2
nCoresRequest = 2
jobResourceRequests :+= "h_vmem=4G"
this.RGLB = RGLB
this.RGPL = RGPL
this.RGPU = RGPU
this.RGSM = RGSM
if (RGCN != null) this.RGCN = RGCN
if (RGDS != null) this.RGDS = RGDS
}
return addOrReplaceReadGroups.output
}
def addMarkDuplicates(inputBams:List[File], outputFile:File, dir:String) : File = {
val markDuplicates = new MarkDuplicates
markDuplicates.input = inputBams
markDuplicates.output = outputFile
markDuplicates.REMOVE_DUPLICATES = false
markDuplicates.metrics = swapExt(dir,outputFile,".bam",".metrics")
markDuplicates.outputIndex = swapExt(dir,markDuplicates.output,".bam",".bai")
markDuplicates.memoryLimit = 2
markDuplicates.jobResourceRequests :+= "h_vmem=4G"
val markDuplicates = new MarkDuplicates {
input = inputBams
output = outputFile
REMOVE_DUPLICATES = false
metrics = swapExt(dir,outputFile,".bam",".metrics")
outputIndex = swapExt(dir,this.output,".bam",".bai")
memoryLimit = 2
jobResourceRequests :+= "h_vmem=4G"
}
add(markDuplicates)
return markDuplicates.output
......
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