From cae4b9b0de177d68a3066bd00c9ef7d2de8ea130 Mon Sep 17 00:00:00 2001 From: carneiro Date: Thu, 27 Jan 2011 19:17:19 +0000 Subject: [PATCH] quick update with the correct CEU trio bam file and it's final location. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5098 348d0f76-0448-11de-a6fe-93d51630548a --- .../oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala index 596f9e885..0dfc7ad3e 100755 --- a/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala @@ -112,7 +112,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass), "WExTrio" -> new Target("NA12878Trio.WEx", b37, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/gsa-scr1/carneiro/prj/trio/data/NA12878Trio.WEx.hg19.recal.bam"), + new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"), new File("/humgen/gsa-scr1/carneiro/prj/trio/snps/NA12878Trio.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, !lowPass) )