diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
index aaddeb28b..bfaebfb91 100644
--- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
+++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
@@ -26,7 +26,7 @@
 package org.broadinstitute.sting.queue.extensions.gatk
 
 import org.broadinstitute.sting.queue.function.scattergather.GatherFunction
-import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction
+import org.broadinstitute.sting.queue.extensions.picard.MergeSamFiles
 import org.broadinstitute.sting.queue.function.{RetryMemoryLimit, QFunction}
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor
 import org.broadinstitute.sting.queue.util.ClassFieldCache
@@ -34,13 +34,17 @@ import org.broadinstitute.sting.queue.util.ClassFieldCache
 /**
  * Merges BAM files using net.sf.picard.sam.MergeSamFiles.
  */
-class BamGatherFunction extends GatherFunction with PicardBamFunction with RetryMemoryLimit {
-  this.javaMainClass = "net.sf.picard.sam.MergeSamFiles"
+class BamGatherFunction extends MergeSamFiles with GatherFunction with RetryMemoryLimit {
   this.assumeSorted = Some(true)
-  protected def inputBams = gatherParts
-  protected def outputBam = originalOutput
 
   override def freezeFieldValues() {
+    this.input = this.gatherParts
+    this.output = this.originalOutput
+    //Left to its own devices (ie, MergeSamFiles.freezeFieldValues), outputIndex
+    //will be in the gather directory.  Ensure that it actually matches this.output
+    if (output != null)
+      outputIndex = new File(output.getParentFile(), output.getName.stripSuffix(".bam") + ".bai")
+    
     val originalGATK = originalFunction.asInstanceOf[CommandLineGATK]
 
     // Whatever the original function can handle, merging *should* do less.