diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 6e1335c3a..efab5c96e 100755
--- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -143,6 +143,8 @@ public class GATKArgumentCollection {
     public DownsamplingMethod getDownsamplingMethod() {
         if(downsamplingType == null && downsampleFraction == null && downsampleCoverage == null)
             return null;
+        if(downsamplingType == null && downsampleCoverage != null)
+            return new DownsamplingMethod(DEFAULT_DOWNSAMPLING_TYPE,downsampleCoverage,null);
         return new DownsamplingMethod(downsamplingType,downsampleCoverage,downsampleFraction);
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
index 4d475b84a..a5902a273 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
@@ -541,8 +541,8 @@ public class LocusIteratorByState extends LocusIterator {
 
         public ReadStateManager(Iterator<SAMRecord> source, DownsamplingMethod downsamplingMethod, Collection<String> sampleNames) {
             this.iterator = new PeekableIterator<SAMRecord>(source);
-            this.downsamplingMethod = downsamplingMethod;
-            switch(downsamplingMethod.type) {
+            this.downsamplingMethod = downsamplingMethod.type != null ? downsamplingMethod : DownsamplingMethod.NONE;
+            switch(this.downsamplingMethod.type) {
                 case BY_SAMPLE:
                     if(downsamplingMethod.toCoverage == null)
                         throw new StingException("Downsampling coverage (-dcov) must be specified when downsampling by sample");