diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java index dd96dfeb9..635a74399 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java @@ -59,7 +59,7 @@ public class BQSRIntegrationTest extends WalkerTest { @Test(dataProvider = "BQSRTest") public void testBQSR(BQSRTest params) { WalkerTestSpec spec = new WalkerTestSpec( - "-T BaseQualityScoreRecalibrator" + + " -T BQSR" + " -R " + params.reference + " -I " + params.bam + " -L " + params.interval + @@ -74,8 +74,8 @@ public class BQSRIntegrationTest extends WalkerTest { @Test public void testBQSRFailWithoutDBSNP() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + b36KGReference + - " -T BaseQualityScoreRecalibrator" + + " -T BQSR" + + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam" + " -L 1:10,000,000-10,200,000" + " --no_plots" +