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methods development pipeline now sports VQSR2. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5478 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-03-18 22:00:46 +00:00
parent c9442e4b21
commit 4e449905d1
1 changed files with 80 additions and 45 deletions
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125
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
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@ -1,3 +1,4 @@
import org.broadinstitute.sting.commandline.Hidden
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
@ -5,7 +6,6 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
// ToDos:
// reduce the scope of the datasets so the script is more nimble
// figure out how to give names to all the Queue-LSF logs (other than Q-1931@node1434-24.out) so that it is easier to find logs for certain steps
// create gold standard BAQ'd bam files, no reason to always do it on the fly
// Analysis to add at the end of the script:
@ -35,9 +35,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
@Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false)
var noBAQ: Boolean = false
@Argument(shortName="noMASK", doc="turns off MASK calculation", required=false)
var noMASK: Boolean = false
@Argument(shortName="eval", doc="adds the VariantEval walker to the pipeline", required=false)
var eval: Boolean = false
@ -50,12 +47,16 @@ class MethodsDevelopmentCallingPipeline extends QScript {
@Argument(shortName="LOCAL_ET", doc="Doesn't use the AWS S3 storage for ET option", required=false)
var LOCAL_ET: Boolean = false
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
logging_level = "INFO";
jarFile = gatkJarFile;
memoryLimit = Some(3);
phone_home = Some(if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3)
}
@Argument(shortName="mbq", doc="The minimum Phred-Scaled quality score threshold to be considered a good base.", required=false)
var minimumBaseQuality: Int = -1
@Argument(shortName="deletions", doc="Maximum deletion fraction allowed at a site to call a genotype.", required=false)
var deletions: Double = -1
@Argument(shortName="sample", doc="Samples to include in Variant Eval", required=false)
var samples: List[String] = Nil
class Target(
val baseName: String,
@ -73,12 +74,13 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val clusterFile = new File(name + ".clusters")
val rawVCF = new File(name + ".raw.vcf")
val rawIndelVCF = new File(name + ".raw.indel.vcf")
val filteredVCF = new File(name + ".filtered.vcf")
val filteredIndelVCF = new File(name + ".filtered.indel.vcf")
val tsRecalibratedVCF = new File(name + ".ts.recalibrated.vcf")
val tsTranchesFile = new File(name + ".ts.tranches")
val goldStandardTsRecalibratedVCF = new File(name + "goldStandard.ts.recalibrated.vcf")
val goldStandardTsTranchesFile = new File(name + "goldStandard.ts.tranches")
val recalibratedVCF = new File(name + ".recalibrated.vcf")
val tranchesFile = new File(name + ".tranches")
val recalFile = new File(name + ".tranches.recal")
val goldStandardRecalibratedVCF = new File(name + "goldStandard.recalibrated.vcf")
val goldStandardTranchesFile = new File(name + "goldStandard.tranches")
val goldStandardRecalFile = new File(name + "goldStandard.tranches.recal")
val cutVCF = new File(name + ".cut.vcf")
val evalFile = new File(name + ".snp.eval")
val evalIndelFile = new File(name + ".indel.eval")
@ -105,7 +107,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val lowPass: Boolean = true
val indels: Boolean = true
val useMask: Boolean = !noMASK
val useCut: Boolean = !noCut
val queueLogDir = ".qlog/"
@ -158,9 +159,9 @@ class MethodsDevelopmentCallingPipeline extends QScript {
var targets: List[Target] = List()
if (!datasets.isEmpty)
for (ds <- datasets)
targets ::= targetDataSets(ds) // Could check if ds was mispelled, but this way an exception will be thrown, maybe it's better this way?
targets ::= targetDataSets(ds)
else // If -dataset is not specified, all datasets are used.
for (targetDS <- targetDataSets.valuesIterator) // for Scala 2.7 or older, use targetDataSets.values
for (targetDS <- targetDataSets.valuesIterator)
targets ::= targetDS
val goldStandard = true
@ -168,21 +169,27 @@ class MethodsDevelopmentCallingPipeline extends QScript {
if( !skipCalling ) {
if (callIndels) add(new indelCall(target), new indelFilter(target), new indelEvaluation(target))
add(new snpCall(target))
add(new snpFilter(target))
add(new GenerateClusters(target, !goldStandard))
add(new VariantRecalibratorNRS(target, !goldStandard))
add(new VQSR(target, !goldStandard))
add(new applyVQSR(target, !goldStandard))
if (!noCut) add(new VariantCut(target))
if (eval) add(new snpEvaluation(target))
}
if ( !skipGoldStandard ) {
add(new GenerateClusters(target, goldStandard))
add(new VariantRecalibratorNRS(target, goldStandard))
add(new VQSR(target, goldStandard))
add(new applyVQSR(target, goldStandard))
}
}
}
def bai(bam: File) = new File(bam + ".bai")
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
logging_level = "INFO";
jarFile = gatkJarFile;
memoryLimit = Some(4);
phone_home = Some(if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3)
}
def bai(bam: File) = new File(bam + ".bai")
val FiltersToIgnore = List("DPFilter", "ABFilter", "ESPStandard", "QualByDepth", "StrandBias", "HomopolymerRun")
// 1.) Unified Genotyper Base
@ -202,6 +209,10 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 1a.) Call SNPs with UG
class snpCall (t: Target) extends GenotyperBase(t) {
if (minimumBaseQuality >= 0)
this.min_base_quality_score = Some(minimumBaseQuality)
if (qscript.deletions >= 0)
this.max_deletion_fraction = Some(qscript.deletions)
this.out = t.rawVCF
this.baq = Some( if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY})
this.analysisName = t.name + "_UGs"
@ -217,29 +228,13 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.jobName = queueLogDir + t.name + ".indelcall"
}
// 2.) Hard Filtering Base
class FilterBase (t: Target) extends VariantFiltration with UNIVERSAL_GATK_ARGS {
// 2.) Hard Filtering for indels
class indelFilter (t: Target) extends VariantFiltration with UNIVERSAL_GATK_ARGS {
this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals)
this.scatterCount = 10
this.filterName ++= List("HARD_TO_VALIDATE")
this.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"")
}
// 2a.) Hard Filter for SNPs (soon to be obsolete)
class snpFilter (t: Target) extends FilterBase(t) {
this.variantVCF = t.rawVCF
this.out = t.filteredVCF
if (useMask) {
this.rodBind :+= RodBind("mask", "Bed", t.maskFile)
this.maskName = "InDel"
}
this.analysisName = t.name + "_VF"
this.jobName = queueLogDir + t.name + ".snpfilter"
}
// 2b.) Hard Filter for Indels
class indelFilter (t: Target) extends FilterBase(t) {
this.variantVCF = t.rawIndelVCF
this.out = t.filteredIndelVCF
this.filterName ++= List("LowQual", "StrandBias", "QualByDepth", "HomopolymerRun")
@ -251,6 +246,43 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.jobName = queueLogDir + t.name + ".indelfilter"
}
// 3.) Variant Quality Score Recalibration - Generate Recalibration table
class VQSR(t: Target, goldStandard: Boolean) extends ContrastiveRecalibrator with UNIVERSAL_GATK_ARGS {
this.memoryLimit = Some(6)
this.intervalsString ++= List(t.intervals)
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } )
this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
if( t.hapmapFile.contains("b37") )
this.rodBind :+= RodBind("1kg", "VCF", omni_b37)
else if( t.hapmapFile.contains("b36") )
this.rodBind :+= RodBind("1kg", "VCF", omni_b36)
if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf"))
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile }
this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile }
this.allPoly = true
this.tranche ++= List("0.1", "0.5", "0.7", "1.0", "1.1", "1.2", "1.5", "1.6", "1.7", "1.8", "1.9", "2.0", "2.1", "2.2", "2.5","3.0", "5.0", "10.0")
this.jobName = queueLogDir + t.name + ".VQSR"
}
// 4.) Apply the recalibration table to the appropriate tranches
class applyVQSR (t: Target, goldStandard: Boolean) extends ApplyRecalibration with UNIVERSAL_GATK_ARGS {
this.memoryLimit = Some(4)
this.intervalsString ++= List(t.intervals)
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } )
this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile}
this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile }
this.fdr_filter_level = Some(2.0)
this.out = t.recalibratedVCF
this.jobName = queueLogDir + t.name + ".applyVQSR"
}
/*
* Obsolete
// 3.) VQSR part1 Generate Gaussian clusters based on truth sites
class GenerateClusters(t: Target, goldStandard: Boolean) extends GenerateVariantClusters with UNIVERSAL_GATK_ARGS {
val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
@ -308,13 +340,15 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.trustAllPolymorphic = true
}
*/
// 5.) Variant Cut filter out the variants marked by recalibration to the 99% tranche
class VariantCut(t: Target) extends ApplyVariantCuts with UNIVERSAL_GATK_ARGS {
this.reference_sequence = t.reference
this.rodBind :+= RodBind("input", "VCF", t.tsRecalibratedVCF )
this.rodBind :+= RodBind("input", "VCF", t.recalibratedVCF )
this.intervalsString ++= List(t.intervals)
this.out = t.cutVCF
this.tranchesFile = t.tsTranchesFile
this.tranchesFile = t.tranchesFile
this.fdr_filter_level = Some(t.trancheTarget)
this.analysisName = t.name + "_VC"
this.jobName = queueLogDir + t.name + ".cut"
@ -333,12 +367,13 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf"))
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
this.sample = samples
}
// 6a.) SNP Evaluation (OPTIONAL) based on the cut vcf
class snpEvaluation(t: Target) extends EvalBase(t) {
if (t.reference == b37 || t.reference == hg19) this.rodBind :+= RodBind("compomni", "VCF", omni_b37)
this.rodBind :+= RodBind("eval", "VCF", if (useCut) {t.cutVCF} else {t.tsRecalibratedVCF} )
this.rodBind :+= RodBind("eval", "VCF", if (useCut) {t.cutVCF} else {t.recalibratedVCF} )
this.out = t.evalFile
this.analysisName = t.name + "_VEs"
this.jobName = queueLogDir + t.name + ".snp.eval"