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Simplifications: removed command-line arguments to control SNP cluster filter parameters. Infer the number of contigs to scatter indel cleaning from the contig list (which we should get rid of too). Changed the PY argument to just Y for specifying the path to the YAML file. Cleaned up command-line argument documentation. See http://iwww.broadinstitute.org/gsa/wiki/index.php/Queue-based_pipeline for a list of remaining issues. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4356 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-09-26 22:50:30 +00:00
parent 9820a12fa5
commit bcc09f5d8c
1 changed files with 44 additions and 50 deletions
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94
scala/qscript/fullCallingPipeline.q
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@ -1,3 +1,4 @@
import net.sf.picard.reference.FastaSequenceFile
import org.broadinstitute.sting.datasources.pipeline.Pipeline import org.broadinstitute.sting.datasources.pipeline.Pipeline
import org.broadinstitute.sting.gatk.DownsampleType import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model
@ -12,59 +13,47 @@ import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType
class fullCallingPipeline extends QScript { class fullCallingPipeline extends QScript {
qscript => qscript =>
@Argument(doc="contigIntervals", shortName="contigIntervals") @Argument(doc="list of contigs in the reference over which indel-cleaning jobs should be scattered (ugly)", shortName="contigIntervals")
var contigIntervals: File = _ var contigIntervals: File = _
@Argument(doc="numContigs", shortName="numContigs") @Argument(doc="the YAML file specifying inputs, interval lists, reference sequence, etc.", shortName="Y")
var numContigs: Int = _ var yamlFile: File = _
@Argument(fullName="pipeline_yaml", shortName="PY", doc="Pipeline YAML file") @Input(doc="path to trigger track (for UnifiedGenotyper)", shortName="trigger", required=false)
var pipelineYamlFile: File = _
@Input(doc="trigger", shortName="trigger", required=false)
var trigger: File = _ var trigger: File = _
@Input(doc="compCEU",shortName="ceu",required=false) @Input(doc="path to refseqTable (for GenomicAnnotator)", shortName="refseqTable")
var comp1KGCEU: File = _
@Input(doc="refseqTable", shortName="refseqTable")
var refseqTable: File = _ var refseqTable: File = _
@Input(doc="Picard FixMateInformation.jar. At the Broad this can be found at /seq/software/picard/current/bin/FixMateInformation.jar. Outside the Broad see http://picard.sourceforge.net/") @Input(doc="path to Picard FixMateInformation.jar. See http://picard.sourceforge.net/ .", required=false)
var picardFixMatesJar: File = _ var picardFixMatesJar: File = new java.io.File("/seq/software/picard/current/bin/FixMateInformation.jar")
@Input(doc="gatk jar") @Input(doc="path to GATK jar")
var gatkJar: File = _ var gatkJar: File = _
@Input(doc="SNP cluster filter -- number SNPs",shortName="snpsInCluster",required=false) @Input(doc="target Ti/Tv ratio for recalibration", shortName="titv", required=true)
var snpsInCluster = 3
@Input(doc="SNP cluster filter -- window size",shortName="snpClusterWindow",required=false)
var snpClusterWindow = 10
@Input(doc="target titv for recalibration",shortName="titv",required=true)
var target_titv: Float = _ var target_titv: Float = _
@Input(doc="downsampling coverage",shortName="dcov",required=false) @Input(doc="per-sample downsampling level",shortName="dcov",required=false)
var downsampling_coverage = 300 var downsampling_coverage = 300
@Input(doc="Number of jobs to scatter UnifiedGenotyper",shortName="snpScatter",required=false) @Input(doc="level of parallelism for UnifiedGenotyper", shortName="snpScatter", required=false)
var num_snp_scatter_jobs = 50 var num_snp_scatter_jobs = 20
@Input(doc="Number of jobs to scatter IndelGenotyperV2",shortName="indelScatter",required=false) @Input(doc="level of parallelism for IndelGenotyperV2", shortName="indelScatter", required=false)
var num_indel_scatter_jobs = 5 var num_indel_scatter_jobs = 5
@Input(doc="Indel-clean BAM files",shortName="clean",required=false) @Input(doc="Skip indel-cleaning for BAM files (for testing only)", shortName="skipCleaning", required=false)
var clean_bam_files = 1 var skip_cleaning = false
@Input(doc="ADPR script") //@Input(doc="ADPR script")
var adprScript: File = _ //var adprScript: File = _
@Input(doc="Sequencing maching name (for use by adpr)") //@Input(doc="Sequencing maching name (for use by adpr)")
var machine: String = _ //var machine: String = _
@Input(doc="Sequencing experiement type (for use by adpr)--Whole_Exome, Whole_Genome, or Hybrid_Selection") //@Input(doc="Sequencing experiement type (for use by adpr)--Whole_Exome, Whole_Genome, or Hybrid_Selection")
var protocol: String = _ //var protocol: String = _
private var pipeline: Pipeline = _ private var pipeline: Pipeline = _
@ -80,16 +69,23 @@ class fullCallingPipeline extends QScript {
def script = { def script = {
pipeline = YamlUtils.load(classOf[Pipeline], qscript.pipelineYamlFile) pipeline = YamlUtils.load(classOf[Pipeline], qscript.yamlFile)
val projectBase: String = qscript.pipeline.getProject.getName val projectBase: String = qscript.pipeline.getProject.getName
val cleanedBase: String = projectBase + ".cleaned" val cleanedBase: String = projectBase + ".cleaned"
val uncleanedBase: String = projectBase + ".uncleaned" val uncleanedBase: String = projectBase + ".uncleaned"
// there are commands that use all the bam files // there are commands that use all the bam files
val recalibratedSamples = qscript.pipeline.getSamples.filter(_.getBamFiles.contains("recalibrated")) val recalibratedSamples = qscript.pipeline.getSamples.filter(_.getBamFiles.contains("recalibrated"))
val adprRScript = qscript.adprScript //val adprRScript = qscript.adprScript
val seq = qscript.machine //val seq = qscript.machine
val expKind = qscript.protocol //val expKind = qscript.protocol
// count number of contigs (needed for indel cleaning parallelism)
var contigCount = 0
for ( line <- scala.io.Source.fromFile(qscript.contigIntervals).getLines ) {
contigCount += 1
}
for ( sample <- recalibratedSamples ) { for ( sample <- recalibratedSamples ) {
// put unclean bams in unclean genotypers in advance, create the extension files // put unclean bams in unclean genotypers in advance, create the extension files
@ -112,7 +108,7 @@ class fullCallingPipeline extends QScript {
realigner.input_file = targetCreator.input_file realigner.input_file = targetCreator.input_file
realigner.intervals = qscript.contigIntervals realigner.intervals = qscript.contigIntervals
realigner.targetIntervals = new java.io.File(targetCreator.out.getAbsolutePath) realigner.targetIntervals = new java.io.File(targetCreator.out.getAbsolutePath)
realigner.scatterCount = qscript.numContigs realigner.scatterCount = contigCount
// may need to explicitly run fix mates // may need to explicitly run fix mates
var fixMates = new PicardBamJarFunction { var fixMates = new PicardBamJarFunction {
@ -157,8 +153,7 @@ class fullCallingPipeline extends QScript {
samtoolsindex.bamFile = cleaned_bam samtoolsindex.bamFile = cleaned_bam
samtoolsindex.analysisName = "index_"+cleaned_bam.getName samtoolsindex.analysisName = "index_"+cleaned_bam.getName
// COMMENT THIS NEXT BLOCK TO SKIP CLEANING if (!qscript.skip_cleaning) {
if (qscript.clean_bam_files == 1) {
if ( realigner.scatterCount > 1 ) { if ( realigner.scatterCount > 1 ) {
add(targetCreator,realigner,samtoolsindex) add(targetCreator,realigner,samtoolsindex)
} else { } else {
@ -177,18 +172,17 @@ class fullCallingPipeline extends QScript {
.toList .toList
// actually make calls // actually make calls
if (qscript.clean_bam_files == 1) { if (!qscript.skip_cleaning) {
// COMMENT THIS NEXT LINE TO AVOID CALLING ON CLEANED FILES
//endToEnd(cleanedBase, cleanBamFiles, adprRscript, seq, expKind) //endToEnd(cleanedBase, cleanBamFiles, adprRscript, seq, expKind)
endToEnd(cleanedBase, cleanBamFiles, seq, expKind) endToEnd(cleanedBase, cleanBamFiles)
} else { } else {
//endToEnd(uncleanedBase, recalibratedBamFiles, adprRscript, seq, expKind) //endToEnd(uncleanedBase, recalibratedBamFiles, adprRscript, seq, expKind)
endToEnd(uncleanedBase, recalibratedBamFiles, seq, expKind) endToEnd(uncleanedBase, recalibratedBamFiles)
} }
} }
//def endToEnd(base: String, bamFiles: List[File], adprthing: File, seqinfo: String, exptype: String) = { //def endToEnd(base: String, bamFiles: List[File], adprthing: File, seqinfo: String, exptype: String) = {
def endToEnd(base: String, bamFiles: List[File], seqinfo: String, exptype: String) = { def endToEnd(base: String, bamFiles: List[File]) = {
// step through the un-indel-cleaned graph: // step through the un-indel-cleaned graph:
// 1a. call snps and indels // 1a. call snps and indels
@ -211,9 +205,9 @@ class fullCallingPipeline extends QScript {
} }
// todo -- add generalize comp inputs // todo -- add generalize comp inputs
if ( qscript.comp1KGCEU != null ) { //if ( qscript.comp1KGCEU != null ) {
snps.rodBind :+= RodBind( "comp1KG_CEU", "VCF", qscript.comp1KGCEU ) // snps.rodBind :+= RodBind( "comp1KG_CEU", "VCF", qscript.comp1KGCEU )
} //}
snps.scatterCount = qscript.num_snp_scatter_jobs snps.scatterCount = qscript.num_snp_scatter_jobs
@ -263,8 +257,8 @@ class fullCallingPipeline extends QScript {
masker.variantVCF = annotated.out masker.variantVCF = annotated.out
masker.rodBind :+= RodBind("mask", "VCF", mergeIndels.out) masker.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
masker.maskName = "NearIndel" masker.maskName = "NearIndel"
masker.clusterWindowSize = Some(qscript.snpClusterWindow) masker.clusterWindowSize = Some(10)
masker.clusterSize = Some(qscript.snpsInCluster) masker.clusterSize = Some(3)
masker.out = swapExt(annotated.out,".vcf",".indel.masked.vcf") masker.out = swapExt(annotated.out,".vcf",".indel.masked.vcf")
masker.analysisName = base+"_Cluster_and_Indel_filter" masker.analysisName = base+"_Cluster_and_Indel_filter"