From de56568ce40f79999c35e26f2cdcb93a6c83f615 Mon Sep 17 00:00:00 2001 From: aaron Date: Thu, 16 Sep 2010 16:30:54 +0000 Subject: [PATCH] Adding the appropriate DbSNP file to the performance tests so they don't exception out. The exception: "org.broadinstitute.sting.utils.exceptions.UserException$CommandLineException: Invalid command line: This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation." git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4293 348d0f76-0448-11de-a6fe-93d51630548a --- .../recalibration/RecalibrationWalkersPerformanceTest.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java index 7b293e5ff..106a027bb 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java @@ -16,6 +16,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest { " -L chr1:1-50,000,000" + " -standard" + " -OQ" + + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod" + " -recalFile /dev/null" + moreArgs, 0, new ArrayList(0)); @@ -30,6 +31,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest { " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + " -standard" + " -OQ" + + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod" + " -recalFile /dev/null" + moreArgs, 0, new ArrayList(0));