diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java
index 9115ce440..2838f361a 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java
@@ -80,6 +80,7 @@ public class MultiSampleCaller extends LocusWalker<String,String>
 
     public String map(RefMetaDataTracker tracker, char ref, LocusContext context) 
 	{
+		if (ref == 'N') { return null; }
 		this.ref = ref;
 		if (tracker.lookup("DBSNP", null) != null) { in_dbsnp = "known"; } else { in_dbsnp = "novel"; }
 		this.MultiSampleCall(context, sample_names);