diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
index fc8daf05a..adf751bdc 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
@@ -190,7 +190,7 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
                     logger.debug("Current list of per-locus features\n" + locusToRefSeqFeatures);
 
                     Map<String, Object> MNPannotations = annotateMNP(vc);
-                    MNPannotations.putAll(vc.getAttributes());
+                    MNPannotations.putAll(RefSeqDataParser.removeRefSeqAttributes(vc.getAttributes())); // remove any RefSeq INFO, since adding it in more thoroughly here
                     vc = VariantContext.modifyAttributes(vc, MNPannotations);
                     writeVCF(vc);
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java
index d5d88f9e3..af3960b1a 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java
@@ -132,6 +132,19 @@ public class RefSeqDataParser {
         return refSeqNameAttribs;
     }
 
+    public static Map<String, Object> removeRefSeqAttributes(Map<String, Object> attributes) {
+        Map<String, Object> removedRefSeqAttributes = new HashMap<String, Object>(attributes);
+
+        Iterator<Map.Entry<String, Object>> attrIt = removedRefSeqAttributes.entrySet().iterator();
+        while (attrIt.hasNext()) {
+            String key = attrIt.next().getKey();
+            if (key.startsWith(REFSEQ_PREFIX))
+                attrIt.remove();
+        }
+
+        return removedRefSeqAttributes;
+    }
+
     private static Map<String, RefSeqEntry> getAllRefSeqEntriesByName(VariantContext vc) {
         Map<String, RefSeqEntry> nameToEntries = new TreeMap<String, RefSeqEntry>();