diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 185880401..e212e07ea 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -18,6 +18,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH --dbsnp " + b36dbSNP129; private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b36dbSNP129; + private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b37dbSNP132; // -------------------------------------------------------------------------------------------------------------- // @@ -28,7 +29,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1, - Arrays.asList("149e6ad9b3fd23551254a691286a96b3")); + Arrays.asList("4bd3e874d071c4df250dce32cf441aab")); executeTest("test MultiSample Pilot1", spec); } @@ -276,7 +277,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { Arrays.asList("e66b7321e2ac91742ad3ef91040daafd")); executeTest("test MultiSample Pilot2 indels with complicated records", spec3); + WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec( + baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation + + "phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1, + Arrays.asList("b6c3f771e8844a64681187ebb2b620f1")); + executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4); + } + }