diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala
index f01044539..d4ee1ad70 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala
@@ -82,8 +82,7 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
    * @param newExtension New extension to append.
    * @return new File with the new extension in the current directory.
    */
-  protected def swapExt(file: File, oldExtension: String, newExtension: String) =
-    new File(file.getName.stripSuffix(oldExtension) + newExtension)
+  protected def swapExt(file: File, oldExtension: String, newExtension: String) = QScriptUtils.swapExt(file, oldExtension, newExtension)
 
   /**
    * Exchanges the extension on a file.
@@ -93,8 +92,7 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
    * @param newExtension New extension to append.
    * @return new File with the new extension in dir.
    */
-  protected def swapExt(dir: File, file: File, oldExtension: String, newExtension: String) =
-    new File(dir, file.getName.stripSuffix(oldExtension) + newExtension)
+  protected def swapExt(dir: File, file: File, oldExtension: String, newExtension: String) = QScriptUtils.swapExt(dir, file, oldExtension, newExtension)
 
   /**
    * Adds one or more command line functions to be run.
@@ -181,4 +179,5 @@ object QScript {
   def resetAddOrder() {
     addOrder = 0
   }
+
 }
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala
index 3fbce2292..9d029133e 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala
@@ -41,6 +41,27 @@ import collection.JavaConversions._
 
 object QScriptUtils {
 
+  /**
+   * Exchanges the extension on a file.
+   * @param file File to look for the extension.
+   * @param oldExtension Old extension to strip off, if present.
+   * @param newExtension New extension to append.
+   * @return new File with the new extension in the current directory.
+   */
+  def swapExt(file: File, oldExtension: String, newExtension: String) =
+    new File(file.getName.stripSuffix(oldExtension) + newExtension)
+
+  /**
+   * Exchanges the extension on a file.
+   * @param dir New directory for the file.
+   * @param file File to look for the extension.
+   * @param oldExtension Old extension to strip off, if present.
+   * @param newExtension New extension to append.
+   * @return new File with the new extension in dir.
+   */
+  def swapExt(dir: File, file: File, oldExtension: String, newExtension: String) =
+    new File(dir, file.getName.stripSuffix(oldExtension) + newExtension)
+
   /**
    * Takes a bam list file and produces a scala sequence with each file allowing the bam list
    * to have empty lines and comment lines (lines starting with #).