From 457c59e737df53ed89621368586dced6194ca0d1 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Tue, 18 Jan 2011 20:50:09 +0000 Subject: [PATCH] Use the sites-only HapMap files in the Methods development pipeline git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5013 348d0f76-0448-11de-a6fe-93d51630548a --- .../rpoplin/MethodsDevelopmentCallingPipeline.scala | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala index a9e278054..f9f32a2ce 100755 --- a/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala @@ -61,9 +61,9 @@ class MethodsDevelopmentCallingPipeline extends QScript { val dbSNP_hg18 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_130_hg18.rod" val dbSNP_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_130_b36.rod" val dbSNP_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_132_b37.leftAligned.vcf" - val hapmap_hg18 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.hg18_fwd.vcf" - val hapmap_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.b36_fwd.vcf" - val hapmap_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf" + val hapmap_hg18 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.hg18_fwd.vcf" + val hapmap_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b36_fwd.vcf" + val hapmap_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" val indelMask_b36 = "/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask.b36.bed" val indelMask_b37 = "/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask.b37.bed" @@ -261,7 +261,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { this.intervalsString ++= List(t.intervals) this.ignoreFilter ++= FiltersToIgnore this.ignoreFilter ++= List("HARD_TO_VALIDATE") - this.target_titv = t.titvTarget + this.target_titv = Some(t.titvTarget) if (t.dbsnpFile.endsWith(".rod")) this.DBSNP = new File(t.dbsnpFile) else if (t.dbsnpFile.endsWith(".vcf"))