diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
index f94a378ad..d8f1cf176 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
@@ -103,6 +103,9 @@ public class SequenomValidationConverter extends RodWalker<VCFRecord,Integer> {
     }
 
     public void onTraversalDone(Integer finalReduce) {
+        if ( sampleNames == null )
+            sampleNames = new TreeSet<String>();
+
         VCFWriter vcfWriter = new VCFWriter(vcfFile);
 
         // set up the info and filter headers
@@ -125,18 +128,20 @@ public class SequenomValidationConverter extends RodWalker<VCFRecord,Integer> {
         hInfo.add(new VCFHeaderLine("ValidationMetrics_SamplesAssayed", String.format("%d", sampleNames.size())));
         System.out.println(String.format("Total number of records processed:\t\t\t%d", numRecords));
         hInfo.add(new VCFHeaderLine("ValidationMetrics_RecordsProcessed", String.format("%d", numRecords)));
-        System.out.println(String.format("Number of Hardy-Weinberg violations:\t\t\t%d (%d%%)", numHWViolations, 100*numHWViolations/numRecords));
-        hInfo.add(new VCFHeaderLine("ValidationMetrics_HardyWeinbergViolations", String.format("\"%d (%d%%)\"", numHWViolations, 100*numHWViolations/numRecords)));
-        System.out.println(String.format("Number of no-call violations:\t\t\t\t%d (%d%%)", numNoCallViolations, 100*numNoCallViolations/numRecords));
-        hInfo.add(new VCFHeaderLine("ValidationMetrics_NoCallViolations", String.format("\"%d (%d%%)\"", numNoCallViolations, 100*numNoCallViolations/numRecords)));
-        System.out.println(String.format("Number of homozygous variant violations:\t\t%d (%d%%)", numHomVarViolations, 100*numHomVarViolations/numRecords));
-        hInfo.add(new VCFHeaderLine("ValidationMetrics_HomVarViolations", String.format("\"%d (%d%%)\"", numHomVarViolations, 100*numHomVarViolations/numRecords)));
-        int goodRecords = numRecords - numHWViolations - numNoCallViolations - numHomVarViolations;
-        System.out.println(String.format("Number of records passing all filters:\t\t\t%d (%d%%)", goodRecords, 100*goodRecords/numRecords));
-        hInfo.add(new VCFHeaderLine("ValidationMetrics_RecordsPassingFilters", String.format("\"%d (%d%%)\"", goodRecords, 100*goodRecords/numRecords)));
-        System.out.println(String.format("Number of passing records that are polymorphic:\t\t%d (%d%%)", numTrueVariants, 100*numTrueVariants/goodRecords));
-        hInfo.add(new VCFHeaderLine("ValidationMetrics_PolymorphicPassingRecords", String.format("\"%d (%d%%)\"", numTrueVariants, 100*numTrueVariants/goodRecords)));
-
+        if ( numRecords > 0 ) {
+            System.out.println(String.format("Number of Hardy-Weinberg violations:\t\t\t%d (%d%%)", numHWViolations, 100*numHWViolations/numRecords));
+            hInfo.add(new VCFHeaderLine("ValidationMetrics_HardyWeinbergViolations", String.format("\"%d (%d%%)\"", numHWViolations, 100*numHWViolations/numRecords)));
+            System.out.println(String.format("Number of no-call violations:\t\t\t\t%d (%d%%)", numNoCallViolations, 100*numNoCallViolations/numRecords));
+            hInfo.add(new VCFHeaderLine("ValidationMetrics_NoCallViolations", String.format("\"%d (%d%%)\"", numNoCallViolations, 100*numNoCallViolations/numRecords)));
+            System.out.println(String.format("Number of homozygous variant violations:\t\t%d (%d%%)", numHomVarViolations, 100*numHomVarViolations/numRecords));
+            hInfo.add(new VCFHeaderLine("ValidationMetrics_HomVarViolations", String.format("\"%d (%d%%)\"", numHomVarViolations, 100*numHomVarViolations/numRecords)));
+            int goodRecords = numRecords - numHWViolations - numNoCallViolations - numHomVarViolations;
+            System.out.println(String.format("Number of records passing all filters:\t\t\t%d (%d%%)", goodRecords, 100*goodRecords/numRecords));
+            hInfo.add(new VCFHeaderLine("ValidationMetrics_RecordsPassingFilters", String.format("\"%d (%d%%)\"", goodRecords, 100*goodRecords/numRecords)));
+            System.out.println(String.format("Number of passing records that are polymorphic:\t\t%d (%d%%)", numTrueVariants, 100*numTrueVariants/goodRecords));
+            hInfo.add(new VCFHeaderLine("ValidationMetrics_PolymorphicPassingRecords", String.format("\"%d (%d%%)\"", numTrueVariants, 100*numTrueVariants/goodRecords)));
+        }
+        
         VCFHeader header = new VCFHeader(hInfo, sampleNames);
         vcfWriter.writeHeader(header);