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 ) {