diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java
index 251c1fe5e..86effd9be 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java
@@ -15,6 +15,8 @@ public class CreateSequenomMask extends RodWalker<Integer, Integer> {
 
 	public Integer map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
         int result = 0;
+        if ( rodData == null ) // apparently, RodWalkers make funky map calls
+            return 0;
 
         Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator();
         while (rods.hasNext()) {