diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
index cf15cc92b..f5e936a09 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
@@ -128,7 +128,16 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
             // add these blocks of work to the work queue
             final ArrayList<ActiveRegion> activeRegions = integrateActiveList( isActiveList );
             logger.debug("Integrated " + isActiveList.size() + " isActive calls into " + activeRegions.size() + " regions." );
-            workQueue.addAll( activeRegions );
+            if( walker.activeRegionOutStream == null ) { 
+                workQueue.addAll( activeRegions ); 
+            } else { // Just want to output the active regions to a file, not actually process them
+                for( final ActiveRegion activeRegion : activeRegions ) {
+                    if( activeRegion.isActive ) {
+                        walker.activeRegionOutStream.println( activeRegion.getLocation() );
+                    }
+                }
+            }
+            
 
             // Since we've sufficiently past this point (or this contig!) in the workQueue we can unload those regions and process them
             if( !workQueue.isEmpty() ) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
index 508aebb5c..98308ee11 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
@@ -40,7 +40,7 @@ import java.util.List;
 public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
 
     @Output(fullName="activeRegionOut", shortName="ARO", doc="Output the active region to this interval list file", required = false)
-    protected PrintStream activeRegionOutStream = null;
+    public PrintStream activeRegionOutStream = null;
 
     @Input(fullName="activeRegionIn", shortName="AR", doc="Use this interval list file as the active regions to process", required = false)
     protected List<IntervalBinding<Feature>> activeRegionBindings = null;