From 27acede64d898ce9731598c1f30ab01fd2163ea6 Mon Sep 17 00:00:00 2001 From: corin Date: Thu, 9 Dec 2010 18:58:56 +0000 Subject: [PATCH] Removing old arguments. We'll now be running with the defaults. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4811 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/fullCallingPipeline.q | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index f4440fe54..d4ee7f4c2 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -209,9 +209,9 @@ class fullCallingPipeline extends QScript { snps.input_file = bamFiles snps.group :+= "Standard" snps.out = new File("SnpCalls", base+".vcf") - snps.standard_min_confidence_threshold_for_emitting = Some(10) - snps.min_mapping_quality_score = Some(20) - snps.min_base_quality_score = Some(20) + //snps.standard_min_confidence_threshold_for_emitting = Some(10) + //snps.min_mapping_quality_score = Some(20) + //snps.min_base_quality_score = Some(20) snps.downsample_to_coverage = Some(qscript.downsampling_coverage) //snps.annotation :+= "QualByDepthV2" snps.DBSNP = qscript.pipeline.getProject.getDbsnpFile