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Updated dbsnp version usage. Calling with 132, but still using 129 for eval to maintain consistant known/novel eval 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4895 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2010-12-22 17:37:27 +00:00
parent 2235245af0
commit e7569cfe6f
1 changed files with 18 additions and 3 deletions
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21
scala/qscript/fullCallingPipeline.q
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@ -65,6 +65,8 @@ class fullCallingPipeline extends QScript {
private var pipeline: Pipeline = _ private var pipeline: Pipeline = _
private var dbsnpType: String = _
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
this.intervals = List(qscript.pipeline.getProject.getIntervalList) this.intervals = List(qscript.pipeline.getProject.getIntervalList)
this.jarFile = qscript.gatkJar this.jarFile = qscript.gatkJar
@ -78,12 +80,21 @@ class fullCallingPipeline extends QScript {
def script = { def script = {
pipeline = YamlUtils.load(classOf[Pipeline], qscript.yamlFile) pipeline = YamlUtils.load(classOf[Pipeline], qscript.yamlFile)
//var dbsnpType: String = _ //figure out how to get it so this is recognized and the whole thing has access to it.
if (qscript.pipeline.getProject.getDbsnpFile.toString.contains("rod")){
dbsnpType = "dbSNP"
} else {
dbsnpType = "VCF"
}
val projectBase: String = qscript.pipeline.getProject.getName val projectBase: String = qscript.pipeline.getProject.getName
if (qscript.skip_cleaning) { if (qscript.skip_cleaning) {
//endToEnd(projectBase + ".uncleaned", "recalibrated", adprRscript, seq, expKind) //endToEnd(projectBase + ".uncleaned", "recalibrated", adprRscript, seq, expKind)
endToEnd(projectBase + ".uncleaned", "recalibrated") endToEnd(projectBase + ".uncleaned", "recalibrated")
} else { } else {
// 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
@ -124,7 +135,7 @@ class fullCallingPipeline extends QScript {
realigner.intervals = Nil realigner.intervals = Nil
realigner.intervalsString = Nil realigner.intervalsString = Nil
realigner.scatterCount = num_cleaner_scatter_jobs min contigs.size realigner.scatterCount = num_cleaner_scatter_jobs min contigs.size
realigner.DBSNP = qscript.pipeline.getProject.getDbsnpFile realigner.rodBind :+= RodBind("dbsnp", dbsnpType, qscript.pipeline.getProject.getDbsnpFile)
realigner.rodBind :+= RodBind("indels", "VCF", swapExt(realigner.reference_sequence.getParentFile, realigner.reference_sequence, "fasta", "1kg_pilot_indels.vcf")) realigner.rodBind :+= RodBind("indels", "VCF", swapExt(realigner.reference_sequence.getParentFile, realigner.reference_sequence, "fasta", "1kg_pilot_indels.vcf"))
// if scatter count is > 1, do standard scatter gather, if not, explicitly set up fix mates // if scatter count is > 1, do standard scatter gather, if not, explicitly set up fix mates
@ -214,7 +225,7 @@ class fullCallingPipeline extends QScript {
//snps.min_base_quality_score = Some(20) //snps.min_base_quality_score = Some(20)
snps.downsample_to_coverage = Some(qscript.downsampling_coverage) snps.downsample_to_coverage = Some(qscript.downsampling_coverage)
//snps.annotation :+= "QualByDepthV2" //snps.annotation :+= "QualByDepthV2"
snps.DBSNP = qscript.pipeline.getProject.getDbsnpFile snps.rodBind :+= RodBind("dbsnp", dbsnpType, qscript.pipeline.getProject.getDbsnpFile)
snps.memoryLimit = Some(6) snps.memoryLimit = Some(6)
//if (qscript.trigger != null) { //if (qscript.trigger != null) {
// snps.trigger_min_confidence_threshold_for_calling = Some(30) // snps.trigger_min_confidence_threshold_for_calling = Some(30)
@ -363,8 +374,12 @@ class fullCallingPipeline extends QScript {
eval.reportLocation = new File("SnpCalls", base+".eval") eval.reportLocation = new File("SnpCalls", base+".eval")
eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R) eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R)
eval.analysisName = base+"_VariantEval" eval.analysisName = base+"_VariantEval"
eval.DBSNP = qscript.pipeline.getProject.getDbsnpFile if(dbsnpType=="VCF"){
eval.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_b37.rod")
} else{
eval.rodBind :+= RodBind("dbsnp", dbsnpType, qscript.pipeline.getProject.getDbsnpFile)
}
add(snps) add(snps)
// 5. Run the ADPR and make pretty stuff // 5. Run the ADPR and make pretty stuff