From a0731eaa81f424d42acc0332673444bd210edad9 Mon Sep 17 00:00:00 2001 From: carneiro Date: Fri, 21 Jan 2011 18:48:31 +0000 Subject: [PATCH] updated NA12878 Trio gold standard data. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5048 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 249d280f6..596f9e885 100755 --- a/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala @@ -113,7 +113,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { "/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-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** + 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) )