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 4ab7d466d..303a975cc 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -310,7 +310,7 @@ public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs,
                 setValue = Utils.join("-", s);
             }
             
-            attributes.put(setKey, setValue);
+            if ( setKey != null ) attributes.put(setKey, setValue);
         }
 
         if ( depth > 0 )
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 9157131e9..2e73c4fd3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -65,7 +65,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="printComplexMerges", shortName="printComplexMerges", doc="Print out interesting sites requiring complex compatibility merging", required=false)
     public boolean printComplexMerges = false;
 
-    @Argument(fullName="setKey", shortName="setKey", doc="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from.", required=false)
+    @Argument(fullName="setKey", shortName="setKey", doc="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from.  Set to null if you don't want the set field emitted.", required=false)
     public String SET_KEY = "set";
 
     private VCFWriter vcfWriter = null;
@@ -84,9 +84,13 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         String[] annotationClassesToUse = { "Standard" };
         engine = new VariantAnnotatorEngine(getToolkit(), annotationClassesToUse, annotationsToUse);
 
+        if ( SET_KEY.toLowerCase().equals("null") )
+            SET_KEY = null;
+
         Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger);
         headerLines.add(new VCFHeaderLine("source", "CombineVariants"));
-        headerLines.add(new VCFInfoHeaderLine(SET_KEY, 1, VCFHeaderLineType.String, "Source VCF for the merged record in CombineVariants"));
+        if ( SET_KEY != null )
+            headerLines.add(new VCFInfoHeaderLine(SET_KEY, 1, VCFHeaderLineType.String, "Source VCF for the merged record in CombineVariants"));
         vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
     }
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index de552971b..31fdf389d 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -40,8 +40,12 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
     }
 
     public void test1InOut(String file, String md5) {
+        test1InOut(file, md5, "");
+    }
+
+    public void test1InOut(String file, String md5, String args) {
          WalkerTestSpec spec = new WalkerTestSpec(
-                 baseTestString(" -priority v1 -B v1,VCF," + validationDataLocation + file),
+                 baseTestString(" -priority v1 -B v1,VCF," + validationDataLocation + file + args),
                  1,
                  Arrays.asList(md5));
          executeTest("testInOut1--" + file, spec);
@@ -57,6 +61,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
 
 
     @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "bbeb813ff559b630570725419e4e1adc"); }
+    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "5039478bd5bb05b4c4e8309cdd887e5f", " -setKey foo"); }
+    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "8502338872d241857379fd25878a7700", " -setKey null"); }
     @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "38b7e64b91c726867a604cf95b9cb10a"); } // official project VCF files in tabix format
 
     @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "4c667935099544a1863e70ae88ddd685"); }