From 76c87c9f1d80777327e8392aecb1b1bcf9a04238 Mon Sep 17 00:00:00 2001 From: carneiro Date: Thu, 19 May 2011 17:45:45 +0000 Subject: [PATCH] trio WGS was creating trio WEX filenames. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5822 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/core/MethodsDevelopmentCallingPipeline.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala index 5367ef7fe..81bd51f9b 100755 --- a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala @@ -125,7 +125,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.WEx.cleaned.recal.bam"), new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf"), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 2.6, 97.0, !lowPass), - "WExTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37, + "WExTrio" -> new Target("CEUTrio.WGS", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37, new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"), new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, 97.0, !lowPass),