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Changes to V2 pipeline and libraries. AB dropped. Cleaning enabled. Project name now properly propagated to intermediate files (instead of the string repr of the object). Indel mask is now expanded prior to filtering at indels. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4769 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-12-01 18:55:48 +00:00
parent 9ac0f98d0d
commit 9f03f09cc9
2 changed files with 47 additions and 17 deletions
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8
scala/qscript/chartl/fullCallingPipelineV2.q
View File

@ -91,7 +91,7 @@ class fullCallingPipelineV2 extends QScript {
}
if ( !qscript.skip_cleaning ) {
cleaningLib.StandardIndelRealign(bamsToClean,qscript.cleaningJobs)
addAll(cleaningLib.StandardIndelRealign(bamsToClean,qscript.cleaningJobs))
}
if (!qscript.skip_cleaning) {
@ -107,7 +107,11 @@ class fullCallingPipelineV2 extends QScript {
var handfilt_vcf = new File(base+"_snps.handfiltered.annotated.vcf")
var indel_vcf = new File(base+"_indel_calls.vcf")
for ( c <- lib.StandardCallingPipeline(bamFiles,indel_vcf,recal_vcf,handfilt_vcf,qscript.target_titv,qscript.refseqTable) ) {
addAll(lib.StandardCallingPipeline(bamFiles,indel_vcf,recal_vcf,handfilt_vcf,qscript.target_titv,qscript.refseqTable))
}
def addAll(clfs: List[CommandLineFunction]) = {
for ( c <- clfs ) {
add(c)
}
}

56
scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
View File

@ -1,16 +1,13 @@
package org.broadinstitute.sting.queue.pipeline
import org.broadinstitute.sting.commandline._
import org.broadinstitute.sting.queue.util._
import java.io.File
import net.sf.picard.reference.FastaSequenceFile
import org.broadinstitute.sting.datasources.pipeline.Pipeline
import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.samtools._
import org.broadinstitute.sting.queue.{QException, QScript}
import collection.JavaConversions._
import org.broadinstitute.sting.utils.yaml.YamlUtils
import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType
import org.broadinstitute.sting.queue.function.CommandLineFunction
class VariantCalling(yaml: File,gatkJar: File) {
vc =>
@ -43,10 +40,18 @@ class VariantCalling(yaml: File,gatkJar: File) {
ug.dt = Some(DownsampleType.BY_SAMPLE)
ug.scatterCount = 50
if ( bams.size > 125 ) {
if ( bams.size > 40 ) {
ug.memoryLimit = Some(4)
}
if ( bams.size > 90 ) {
ug.memoryLimit = Some(6)
}
if ( bams.size > 140 ) {
ug.memoryLimit = Some(8)
}
return ug
}
@ -89,6 +94,10 @@ class VariantCalling(yaml: File,gatkJar: File) {
//cv.priority = (igList.foldLeft[List[String]](Nil)( (prLs, ig) => prLs ::: List(swapExt(ig.out,".vcf","").getAbsolutePath))).mkString(",")
cv.rodBind = igList.map[RodBind,List[RodBind]](ig => new RodBind(swapExt(ig.out,".vcf","").getName,"VCF",ig.out))
if ( igList.size > 50 ) {
cv.memoryLimit = Some(4)
}
return cv
}
@ -127,8 +136,6 @@ class VariantCalling(yaml: File,gatkJar: File) {
hFil.variantVCF = snps
hFil.filterExpression :+= "QD<5"
hFil.filterName :+= "LowQualByDepth"
hFil.filterExpression :+= "AB>0.75"
hFil.filterName :+= "HighAlleleBalance"
hFil.filterExpression :+= "SB>-0.10"
hFil.filterName :+= "HighStrandBias"
@ -143,7 +150,6 @@ class VariantCalling(yaml: File,gatkJar: File) {
genC.use_annotation :+= "QD"
genC.use_annotation :+= "SB"
genC.use_annotation :+= "HaplotypeScore"
genC.use_annotation :+= "AB"
genC.use_annotation :+= "HRun"
return genC
@ -283,15 +289,32 @@ class VariantCalling(yaml: File,gatkJar: File) {
return commands
}
def StandardCallingPipeline(bams: List[File], indelOut: File, recalOut: File, handFilteredOut: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = {
var commands : List[CommandLineGATK] = Nil
class VCF2Mask extends CommandLineFunction {
@Input(doc="the indel vcf") var indel_vcf : File = _
@Argument(doc="the window size") var win_size : Int = 2
@Output(doc="the mask bed") var out_mask : File = _
def commandLine = { "grep PASS %s | awk '{print $1,$2-%d,$2+%d}' > %s".format(indel_vcf.getAbsolutePath,win_size,win_size,out_mask.getAbsolutePath) }
}
def IndelVCF2Mask(vcf: File, size: Int) : VCF2Mask = {
var masker: VCF2Mask = new VCF2Mask()
masker.indel_vcf = vcf
masker.win_size = size
masker.out_mask = swapExt(vcf,".vcf",".indel_mask.bed")
return masker
}
def StandardCallingPipeline(bams: List[File], indelOut: File, recalOut: File, handFilteredOut: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineFunction] = {
var commands : List[CommandLineFunction] = Nil
var dir = ""
if ( recalOut.getParent != null ) {
dir = recalOut.getParent+"/"
}
var raw_snp = new File(dir+vc.attributes.getProject+".raw_snps.vcf")
var raw_snp = new File(dir+vc.attributes.getProject.getName+".raw_snps.vcf")
var ug = StandardUnifiedGenotyper(bams, raw_snp)
commands :+= ug
@ -299,10 +322,13 @@ class VariantCalling(yaml: File,gatkJar: File) {
var raw_indel = indelOut
var ig = StandardIndelCalls(bams,raw_indel)
var indel_mask : VCF2Mask = IndelVCF2Mask(indelOut,5)
commands ++= ig
commands :+= indel_mask
var prefilt_snp = swapExt(raw_snp,".vcf",".indel_filtered.vcf")
var iFilt = StandardFilterAtIndels(raw_snp,raw_indel,prefilt_snp)
var iFilt = StandardFilterAtIndels(raw_snp,indel_mask.out_mask,prefilt_snp)
commands :+= iFilt