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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
This commit is contained in:
aaron 2010-09-16 16:30:54 +00:00
parent 782e0018e4
commit de56568ce4
1 changed files with 2 additions and 0 deletions
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2
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
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@ -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<String>(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<String>(0));