diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java index 08735a74c..9b659a89b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java @@ -63,28 +63,31 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { private static String CEUtrioPopPriorsTest = privateTestDir + "CEUtrioPopPriorsTest.vcf"; @Test(enabled = true) + //use the first 20 variants to save time; they have a nice range of AC from 4 to over 4000 public void testUsingDiscoveredAF() { WalkerTestSpec spec = new WalkerTestSpec( "-T CalculateGenotypePosteriors --no_cmdline_in_header" + " -o %s" + " -R " + b37KGReference + - " -L 20:10,000,000-10,100,000" + + " -L 20:10,000,000-10,001,432" + " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf", 1, - Arrays.asList("75c4b1baba3071047e4629c8e81ddea1")); + Arrays.asList("afe5c06ef62612e4c663a3f8e9f5cd60")); executeTest("testUsingDiscoveredAF", spec); } @Test(enabled = true) + //this test ignores discovered AC and has no external priors, so it should only apply the PP tag with values the same as PLs + //only test the first 20 variants to save time public void testMissingPriors() { WalkerTestSpec spec = new WalkerTestSpec( "-T CalculateGenotypePosteriors --no_cmdline_in_header -useACoff" + " -o %s" + " -R " + b37KGReference + - " -L 20:10,000,000-10,100,000" + + " -L 20:10,000,000-10,001,432" + " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf", 1, - Arrays.asList("5a2d7481fc69b97033f8c3ae9c0bdd20")); + Arrays.asList("de153b79fd1c0e1c1f769ec4a9fb01e0")); executeTest("testMissingPriors", spec); }