diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java
index 24a735422..58d678956 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java
@@ -125,7 +125,9 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
 
         ArrayList<VCFGenotypeEncoding> genotypeEncodings = new ArrayList<VCFGenotypeEncoding>();
         for (VCFGenotypeEncoding allele : genotypeEncodingSet) {
-            genotypeEncodings.add(allele);
+            if (!allele.getBases().equalsIgnoreCase(".")) {
+                genotypeEncodings.add(allele);
+            }
         }
 
         VCFRecord subset = new VCFRecord(record.getReference(),