diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 771468902..c181fd470 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -164,7 +164,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     @Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=false)
     protected boolean DEPRECATED_REALIGN_MATES = false;
 
-    @Deprecated
+    //    @Deprecated
+    @Hidden
     @Argument(fullName="useOnlyKnownIndels", shortName="knownsOnly", doc="This argument is no longer used. See --consensusDeterminationModel instead.", required=false)
     protected boolean DEPRECATED_KNOWNS_ONLY = false;
 
@@ -229,6 +230,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
     public void initialize() {
 
+	if ( DEPRECATED_KNOWNS_ONLY )
+	    consensusModel = ConsensusDeterminationModel.KNOWNS_ONLY;
+
         if ( LOD_THRESHOLD < 0.0 )
             throw new RuntimeException("LOD threshold cannot be a negative number");
         if ( MISMATCH_THRESHOLD <= 0.0 || MISMATCH_THRESHOLD > 1.0 )