diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
index d0d28601c..05bd37ec5 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
@@ -170,9 +170,13 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
         return new Interval(target.getContig(), (int) target.getStart(), (int) target.getStop());
     }
 
+    IndexedFastaSequenceFile seqFile = null;
+
     private double calculateGC(GenomeLoc target) {
         try {
-            IndexedFastaSequenceFile seqFile = new IndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
+            if (seqFile == null) {
+                seqFile = new IndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
+            }
             ReferenceSequence refSeq = seqFile.getSubsequenceAt(target.getContig(),target.getStart(), target.getStop());