zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

added optional argument -cut to apply the variant cut to the ts recalibrated vcf. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5183 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-02-03 17:34:40 +00:00
parent 5398cf620a
commit 7af003666d
1 changed files with 35 additions and 16 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

51
scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala
View File

@ -1,8 +1,5 @@
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
import org.broadinstitute.sting.queue.QScript
import org.apache.commons.io.FilenameUtils;
class MethodsDevelopmentCallingPipeline extends QScript {
qscript =>
@ -31,6 +28,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
@Argument(shortName="eval", doc="adds the VariantEval walker to the pipeline", required=false)
var eval: Boolean = false
@Argument(shortName="cut", doc="adds the ApplyVariantCut walker to the pipeline", required=false)
var cut: Boolean = false
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(3); }
@ -50,7 +49,11 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val rawVCF = new File(name + ".raw.vcf")
val filteredVCF = new File(name + ".filtered.vcf")
val titvRecalibratedVCF = new File(name + ".titv.recalibrated.vcf")
val titvTranchesFile = new File(name + ".titv.tranches")
val tsRecalibratedVCF = new File(name + ".ts.recalibrated.vcf")
val tsTranchesFile = new File(name + ".ts.tranches")
val cutVCF = new File(name + ".cut.vcf")
val evalFile = new File(name + ".eval")
val goldStandardName = qscript.outputDir + "goldStandard/" + baseName
val goldStandardClusterFile = new File(goldStandardName + ".clusters")
}
@ -111,10 +114,10 @@ class MethodsDevelopmentCallingPipeline extends QScript {
new File("/humgen/1kg/processing/pipeline_test_bams/EUR.363sample.Nov2010.chr20.bam"),
new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass),
"WExTrio" -> new Target("CEUTrio.WEx", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"),
new File("/humgen/gsa-scr1/carneiro/prj/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"),
"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass)
"WExTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"),
new File("/humgen/gsa-scr1/carneiro/prj/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"),
"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass)
)
@ -137,6 +140,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
add(new GenerateVariantClusters(target, !goldStandard))
add(new VariantRecalibratorTiTv(target, !goldStandard))
add(new VariantRecalibratorNRS(target, !goldStandard))
if (cut) add (new VariantCut(target))
if (eval) add(new VariantEvaluation(target))
}
if ( !skipGoldStandard ) {
@ -231,31 +235,46 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 4a.) Choose VQSR tranches based on novel ti/tv
class VariantRecalibratorTiTv(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) {
this.tranche ++= List("0.1", "1.0", "10.0", "100.0")
this.out = new File(this.name + ".titv.recalibrated.vcf")
this.tranchesFile = new File(this.name + ".titv.tranches")
this.out = t.titvRecalibratedVCF
this.tranchesFile = t.titvTranchesFile
}
// 4b.) Choose VQSR tranches based on sensitivity to truth set
class VariantRecalibratorNRS(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) {
this.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY)
this.tranche ++= List("0.1", "1.0", "10.0", "100.0")
this.out = new File(this.name + ".ts.recalibrated.vcf")
this.out = t.tsRecalibratedVCF
this.priorDBSNP = Some(2.0)
this.priorHapMap = Some(2.0)
this.prior1KG = Some(2.0)
this.tranchesFile = new File(this.name + ".ts.tranches")
this.tranchesFile = t.tsTranchesFile
}
// 5.) Variant Evaluation (OPTIONAL!) based on the sensitivity recalibrated vcf
// 5.) Variant Cut (OPTIONAL!) filter out the variants marked by recalibration to the 99% tranche
class VariantCut(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.ApplyVariantCuts with UNIVERSAL_GATK_ARGS {
this.reference_sequence = t.reference
this.rodBind :+= RodBind("input", "VCF", t.tsRecalibratedVCF )
this.analysisName = t.name + "_VC"
this.intervalsString ++= List(t.intervals)
this.out = t.cutVCF
this.tranchesFile = t.tsTranchesFile
this.fdr_filter_level = Some(1.0)
if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf"))
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
}
// 6.) Variant Evaluation (OPTIONAL!) based on the sensitivity recalibrated vcf
class VariantEvaluation(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS {
val name: String = t.name
this.reference_sequence = t.reference
this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)
this.rodBind :+= RodBind("eval", "VCF", t.tsRecalibratedVCF)
this.analysisName = name + "_VR"
this.rodBind :+= RodBind("eval", "VCF", if (cut) {t.cutVCF} else {t.tsRecalibratedVCF} )
this.analysisName = name + "_VE"
this.intervalsString ++= List(t.intervals)
this.EV ++= List("GenotypeConcordance", "PrintMissingComp")
this.out = new File(this.name + ".eval")
this.EV ++= List("GenotypeConcordance")
this.out = t.evalFile
if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf"))