diff --git a/src/test/java/org/broadinstitute/hellbender/engine/GATKToolUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/GATKToolUnitTest.java
index 98658958e77..0c176332a6a 100644
--- a/src/test/java/org/broadinstitute/hellbender/engine/GATKToolUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/engine/GATKToolUnitTest.java
@@ -642,16 +642,6 @@ public void testGetAllAnnotations() {
         }
     }
 
-    @Test
-    public void testConfigureAnnotationPackages(){
-        String[] args = {"--"+StandardArgumentDefinitions.ENABLE_ALL_ANNOTATIONS,
-                "--"+StandardArgumentDefinitions.GATK_CONFIG_FILE_OPTION, publicTestDir + "org/broadinstitute/hellbender/cmdline/GATKPlugin/changePluginPackages.properties"};
-
-        final TestGATKToolWithVariants tool = createTestVariantTool(args);
-        Collection<Annotation> annots = tool.makeVariantAnnotations();
-        Assert.assertEquals(annots.iterator().next().getClass(), TestAnnotation.class);
-    }
-
     @Test
     public void testExcludeAnnotation(){
         String[] args = {"--"+StandardArgumentDefinitions.ENABLE_ALL_ANNOTATIONS, "-AX", "Coverage"};