diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 4efc0b8a9..001687b74 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -45,6 +45,9 @@ public class UnifiedArgumentCollection {
     public Double PCR_error = DiploidSNPGenotypeLikelihoods.DEFAULT_PCR_ERROR_RATE;
 
     // control the output
+    @Argument(fullName = "sites_only", shortName = "sites_only", doc = "Should we output just sites without genotypes (i.e. only the first 8 columns of the VCF)?", required = false)
+    public boolean SITES_ONLY = false;
+
     @Argument(fullName = "genotype", shortName = "genotype", doc = "Should we output confident genotypes (i.e. including ref calls) or just the variants?", required = false)
     public boolean GENOTYPE_MODE = false;
 
@@ -106,6 +109,7 @@ public class UnifiedArgumentCollection {
         uac.GLmodel = GLmodel;
         uac.heterozygosity = heterozygosity;
         uac.PCR_error = PCR_error;
+        uac.SITES_ONLY = SITES_ONLY;
         uac.GENOTYPE_MODE = GENOTYPE_MODE;
         uac.ALL_BASES_MODE = ALL_BASES_MODE;
         uac.NO_SLOD = NO_SLOD;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index c6f6d986a..bf0879a73 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -129,6 +129,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         annotationEngine = new VariantAnnotatorEngine(getToolkit(), Arrays.asList(annotationClassesToUse), annotationsToUse);
         UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples);
 
+        if ( UAC.SITES_ONLY )
+            samples.clear();
+
         // initialize the header
         writer.writeHeader(new VCFHeader(getHeaderInfo(), samples)) ;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 9ea341d92..d4f009937 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -400,6 +400,9 @@ public class UnifiedGenotyperEngine {
             vcCall = variantContexts.iterator().next(); // we know the collection will always have exactly 1 element.
         }
 
+        if ( UAC.SITES_ONLY )
+            vcCall = VariantContext.modifyGenotypes(vcCall, null);
+
         VariantCallContext call = new VariantCallContext(vcCall, passesCallThreshold(phredScaledConfidence, atTriggerTrack));
         call.setRefBase(refContext.getBase());
         return call;