diff --git a/build.xml b/build.xml
index ccd7a8aa0..a288f2927 100644
--- a/build.xml
+++ b/build.xml
@@ -547,10 +547,12 @@
 
     <target name="vcf.jar" depends="gatk.compile,init.jar">
         <jar jarfile="${dist.dir}/vcf.jar">
-	    <classfileset dir="${java.classes}">
-	      <rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/codecs/vcf/**/*.class" />
-	      <rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/variantcontext/**/*.class" />
-	    </classfileset>
+            <fileset dir="${java.classes}">
+              <include name="**/utils/codecs/**/*.class"/>
+              <include name="**/utils/variantcontext/**/*.class"/>
+              <include name="org/broadinstitute/sting/utils/exceptions/**"/>
+	      <include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
+            </fileset>
         </jar>
     </target>
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index 72058ba7b..e83434037 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -130,6 +130,10 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                     nVariantLoci++;
                     nMixed++;
                     break;
+                case SYMBOLIC:
+                    // ignore symbolic alleles, but don't fail
+                    // todo - consistent way of treating symbolic alleles thgoughout codebase?
+                    break;
                 default:
                     throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
             }