diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
index f8915b078..cf1a1f2d2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
@@ -57,7 +57,7 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
     @Override
     public void initialize() {
         intervals = parseIntervals(intervalsSource);
-        currentInterval = intervals.removeFirst();
+        currentInterval = (intervals.size() > 0 ? intervals.removeFirst() : null);
     }
 
     @Override