diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala
index db90b5321..00b42546b 100644
--- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala
@@ -7,20 +7,26 @@ import java.lang.String
 /**
  * Used to provide -B rodBind arguments to the GATK.
  */
-class RodBind(var trackName: String, var trackType: String, path: String) extends File(path) with FileExtension {
+class RodBind(var trackName: String, var trackType: String, path: String, val tag: String) extends File(path) with FileExtension {
+  def this(trackName: String, trackType: String, path: String) =
+    this(trackName, trackType, path, null)
+  def this(trackName: String, trackType: String, file: File, tag: String) =
+    this(trackName, trackType, file.getPath, tag)
   def this(trackName: String, trackType: String, file: File) =
-    this(trackName, trackType, file.getPath)
+    this(trackName, trackType, file.getPath, null)
   require(trackName != null, "RodBind trackName cannot be null")
   require(trackType != null, "RodBind trackType cannot be null")
-  def withPath(newPath: String) = new RodBind(trackName, trackType, newPath)
+  def withPath(newPath: String) = new RodBind(trackName, trackType, newPath, tag)
 }
 
 /**
  * Used to provide -B rodBind arguments to the GATK.
  */
 object RodBind {
-  def apply(trackName: String, trackType: String, path: String) = new RodBind(trackName, trackType, path)
-  def apply(trackName: String, trackType: String, file: File) = new RodBind(trackName, trackType, file)
+  def apply(trackName: String, trackType: String, path: String, tag: String) = new RodBind(trackName, trackType, path, tag)
+  def apply(trackName: String, trackType: String, path: String) = new RodBind(trackName, trackType, path, null)
+  def apply(trackName: String, trackType: String, file: File, tag: String) = new RodBind(trackName, trackType, file, tag)
+  def apply(trackName: String, trackType: String, file: File) = new RodBind(trackName, trackType, file, null)
 
   /**
    * Formats the rod binding on the command line.
@@ -33,6 +39,8 @@ object RodBind {
    */
   def formatCommandLine(cmdLineParam: String)(prefix: String, value: Any, suffix: String) = {
     value match {
+      case rodBind: RodBind if (rodBind.tag != null) =>
+        " %s:%s,%s,%s %s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.getPath, rodBind.tag)
       case rodBind: RodBind =>
         " %s:%s,%s %s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.getPath)
     }