diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 8f23ae6c7..832616731 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -135,6 +135,14 @@ public class GenomeLocParser {
         return true;
     }
 
+    /**
+     * A package-protected method that can be used by the test system to reset the sequence dictionary
+     * being used.  Use this method sparingly. 
+     */
+    static void clearRefContigOrdering() {
+        contigInfo = null;
+    }
+
     /**
      * parse a genome interval, from a location string
      *
diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java
index fcd9ac2f0..6f8866f97 100755
--- a/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -28,6 +28,7 @@ package org.broadinstitute.sting;
 import junit.framework.Assert;
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
+import org.broadinstitute.sting.utils.GenomeLocParserTestUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.Utils;
@@ -274,6 +275,8 @@ public class WalkerTest extends BaseTest {
      * @return a pair of file and string lists
      */
     private Pair<List<File>, List<String>> executeTest(String name, List<String> md5s, List<File> tmpFiles, String args, Class expectedException) {
+        GenomeLocParserTestUtils.clearSequenceDictionary();
+
         CommandLineGATK instance = new CommandLineGATK();
         String[] command;
 
diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocParserTestUtils.java b/java/test/org/broadinstitute/sting/utils/GenomeLocParserTestUtils.java
new file mode 100644
index 000000000..89b527a38
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/utils/GenomeLocParserTestUtils.java
@@ -0,0 +1,39 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils;
+
+/**
+ * A suite of utilities for working with the GenomeLocParser
+ * in the context of the sequence dictionary.
+ */
+public class GenomeLocParserTestUtils {
+    /**
+     * Clear out the sequence dictionary associated with
+     * the genomeloc creator.
+     */
+    public static void clearSequenceDictionary() {
+        GenomeLocParser.clearRefContigOrdering();    
+    }
+}