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HC test should continue using 3 alt alleles for indels

This commit is contained in:
Eric Banks 2012-10-05 02:03:34 -04:00
parent c66ef17cd0
commit f840d9edbd
1 changed files with 1 additions and 1 deletions
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protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -31,7 +31,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeCallerMultiSampleGGA() { public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "71bec55320a2f07af0d54be9d7735322"); HCTest(CEUTRIO_BAM, "--max_alternate_alleles_for_indels 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "71bec55320a2f07af0d54be9d7735322");
} }
private void HCTestComplexVariants(String bam, String args, String md5) { private void HCTestComplexVariants(String bam, String args, String md5) {