diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index e3abd7547..881ebabae 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -249,6 +249,8 @@ public class VariantContextUtils {
 
 
     public static double computeHardyWeinbergPvalue(VariantContext vc) {
+        if ( vc.getChromosomeCount() == 0 )
+            return 0.0;
         return HardyWeinbergCalculation.hwCalculate(vc.getHomRefCount(), vc.getHetCount(), vc.getHomVarCount());
     }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java
index df971cced..f94cd3c00 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java
@@ -158,12 +158,12 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
         double hetProp = (double)vContext.getHetCount() / (double)vContext.getNSamples();
         double homVarProp = (double)vContext.getHomVarCount() / (double)vContext.getNSamples();
 
-        if ( hwScore > maxHardy ) {
-            record.setFilterString("HardyWeinbergViolation");
-            numHWViolations++;
-        } else if ( noCallProp > maxNoCall ) {
+        if ( noCallProp > maxNoCall ) {
             record.setFilterString("HighNoCallRate");
             numNoCallViolations++;
+        } else if ( hwScore > maxHardy ) {
+            record.setFilterString("HardyWeinbergViolation");
+            numHWViolations++;
         } else if ( homVarProp > maxHomNonref) {
             record.setFilterString("TooManyHomVars");
             numHomVarViolations++;
@@ -183,6 +183,9 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
         infoMap.put(VCFRecord.ALLELE_NUMBER_KEY, String.format("%d", vContext.getChromosomeCount()));
         record.addInfoFields(infoMap);
 
+        // add the id
+        record.setID(plinkRod.getVariantName());
+
         return record;
     }