diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
index 76f8cbc2e..3d3299053 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -387,11 +387,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     @Argument(fullName="useAllelesTrigger", shortName="allelesTrigger", doc = "Use additional trigger on variants found in an external alleles file", required=false)
     protected boolean USE_ALLELES_TRIGGER = false;
 
-
-    @Advanced
-    @Argument(fullName="mergeVariantsViaLD", shortName="mergeVariantsViaLD", doc="Merge variants together into block substitutions if they are in strong local LD", required = false)
-    protected boolean mergeVariantsViaLD = false;
-
     /**
      * As of GATK 3.3, HaplotypeCaller outputs physical (read-based) information (see version 3.3 release notes and documentation for details). This argument disables that behavior.
      */
@@ -495,6 +490,22 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
 
     ReferenceConfidenceModel referenceConfidenceModel = null;
 
+
+    ////////////////////////////////////////////////////////////////////////
+    //// Deprecated Arguments					                        ////
+    //// Keeping them here is meant to provide informative error messages //
+    //// when an argument has been put out of service		            ////
+    ////////////////////////////////////////////////////////////////////////
+    /**
+     * @deprecated
+     * Deprecated: 2015-04-01, J.White
+     * mergeVariantsViaLD = false made final
+     */
+    @Hidden
+    @Deprecated
+    @Argument(fullName="mergeVariantsViaLD", shortName="mergeVariantsViaLD", doc="DEPRECATED; This argument is no longer used in GATK versions 3.4 and newer. Please see the online documentation for the latest usage recommendations.", required = false)
+    static final boolean mergeVariantsViaLD = false;
+
     //---------------------------------------------------------------------------------------------------------------
     //
     // initialize
@@ -654,7 +665,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         // create our likelihood calculation engine
         likelihoodCalculationEngine = createLikelihoodCalculationEngine();
 
-        final MergeVariantsAcrossHaplotypes variantMerger = mergeVariantsViaLD ? new LDMerger(HCAC.DEBUG, 10, 1) : new MergeVariantsAcrossHaplotypes();
+        final MergeVariantsAcrossHaplotypes variantMerger = new MergeVariantsAcrossHaplotypes();
 
         genotypingEngine.setCrossHaplotypeEventMerger(variantMerger);
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 2a3d72839..0b6bfd201 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -444,8 +444,22 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
                         1, UserException.CommandLineException.class));
     }
 
+    @Test 
+    public void testHaplotypeCallerMergeVariantsViaLDException(){
+        executeTest("HaplotypeCallerMergeVariantsViaLDException",
+                new WalkerTest.WalkerTestSpec(
+                        " -T HaplotypeCaller" +
+                                " -R " + REF +
+                                " -I " + NA12878_BAM +
+                                " -L " + INTERVALS_FILE +
+				" --mergeVariantsViaLD " +
+                                " -o %s",
+                        1, UserException.DeprecatedArgument.class));
+    }
+
     @Test
     public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{
         HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "481787c9275ab9f2e2b53025805472b7");
     }
 }
+