diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index fe5ac3b94..f6af8b82d 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -324,7 +324,7 @@ public class GenomeLocParser {
             File inputFile = new File(file_name);
             
             // sometimes we see an empty file passed as a parameter, if so return an empty list
-            if (inputFile.length() < 1) return new ArrayList<GenomeLoc>();
+            if (inputFile.exists() && inputFile.length() < 1) return new ArrayList<GenomeLoc>();
             IntervalList il = IntervalList.fromFile(inputFile);
             
             // iterate through the list of merged intervals and add then as GenomeLocs