diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
index 041db79fc..6f8d0384c 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
@@ -86,6 +86,12 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
             if ( vc_eval == null || vc_eval.isFiltered() )
                 return 0;
 
+             if (vc_eval.getType() != VariantContext.Type.SNP)
+                     return 0;
+
+             if (vc_eval.getAlleles().size()!= 2)
+                     return 0;
+             
             // output marker ID to Beagle input file
             beagleWriter.print(String.format("%s ", vc_eval.getLocation().toString()));