diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 3d375aba2..5787b591f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1343,6 +1343,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         return (int)stop;
     }
 
+    private boolean hasSymbolicAlleles() {
+        for (Allele a: getAlleles()) {
+            if (a.isSymbolic()) {
+                return true;
+            }
+        }
+        return false;
+    }
+
     public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, byte inputRefBase, boolean refBaseShouldBeAppliedToEndOfAlleles) {
         Allele refAllele = inputVC.getReference();
 
@@ -1352,7 +1361,9 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         // We need to pad a VC with a common base if the length of the reference allele is less than the length of the VariantContext.
         // This happens because the position of e.g. an indel is always one before the actual event (as per VCF convention).
         long locLength = (inputVC.getEnd() - inputVC.getStart()) + 1;
-        if (refAllele.length() == locLength)
+        if (inputVC.hasSymbolicAlleles())
+            padVC = true;
+        else if (refAllele.length() == locLength)
             padVC = false;
         else if (refAllele.length() == locLength-1)
             padVC = true;