From 3a2e32eef3e813bfe37c114ef6479a6278d057d8 Mon Sep 17 00:00:00 2001 From: carneiro Date: Fri, 20 May 2011 16:44:25 +0000 Subject: [PATCH] wex is wex, wgs is wgs.... i think i got it right this time. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5828 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/core/MethodsDevelopmentCallingPipeline.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala index 81bd51f9b..7b4514c40 100755 --- a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala @@ -125,11 +125,11 @@ 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.WGS", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37, + "WExTrio" -> new Target("CEUTrio.WEx", 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), - "WGSTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37, + "WGSTrio" -> new Target("CEUTrio.WGS", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37, new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.bwa.cleaned.recal.bam"), new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass),