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Updated pipeline script to include dbSnp for UG 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4679 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2010-11-15 18:09:47 +00:00
parent 302e8f0239
commit a64f693b20
1 changed files with 7 additions and 6 deletions
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13
scala/qscript/fullCallingPipeline.q
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@ -213,13 +213,14 @@ 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
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)
snps.rodBind :+= RodBind("trigger", "VCF", qscript.trigger) // snps.rodBind :+= RodBind("trigger", "VCF", qscript.trigger)
// TODO: triggers need to get a name for comp-ing them if not dbSNP? // // TODO: triggers need to get a name for comp-ing them if not dbSNP?
snps.rodBind :+= RodBind( "compTrigger", "VCF", qscript.trigger ) // snps.rodBind :+= RodBind( "compTrigger", "VCF", qscript.trigger )
} //}
// todo -- add generalize comp inputs // todo -- add generalize comp inputs
//if ( qscript.comp1KGCEU != null ) { //if ( qscript.comp1KGCEU != null ) {