From a64f693b2082df873149c7959cc8665a9fdc1298 Mon Sep 17 00:00:00 2001 From: corin Date: Mon, 15 Nov 2010 18:09:47 +0000 Subject: [PATCH] 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 --- scala/qscript/fullCallingPipeline.q | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index a49ac1096..a24ca56b1 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -213,13 +213,14 @@ class fullCallingPipeline extends QScript { snps.min_base_quality_score = Some(20) snps.downsample_to_coverage = Some(qscript.downsampling_coverage) //snps.annotation :+= "QualByDepthV2" + snps.dbsnp =qscript.pipeline.getProject.getDbsnpFile - if (qscript.trigger != null) { - snps.trigger_min_confidence_threshold_for_calling = Some(30) - snps.rodBind :+= RodBind("trigger", "VCF", qscript.trigger) - // TODO: triggers need to get a name for comp-ing them if not dbSNP? - snps.rodBind :+= RodBind( "compTrigger", "VCF", qscript.trigger ) - } + //if (qscript.trigger != null) { + // snps.trigger_min_confidence_threshold_for_calling = Some(30) + // snps.rodBind :+= RodBind("trigger", "VCF", qscript.trigger) + // // TODO: triggers need to get a name for comp-ing them if not dbSNP? + // snps.rodBind :+= RodBind( "compTrigger", "VCF", qscript.trigger ) + //} // todo -- add generalize comp inputs //if ( qscript.comp1KGCEU != null ) {