diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
index ac3388795..0edcb22e1 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
@@ -80,7 +80,7 @@ public class SingleSampleCompressor {
     }
 
     public Set<GATKSAMRecord> closeVariantRegions(CompressionStash regions) {
-        return slidingWindow.closeVariantRegions(regions);
+        return slidingWindow == null ? Collections.<GATKSAMRecord>emptySet() : slidingWindow.closeVariantRegions(regions);
     }
 
 }