diff --git a/scala/qscript/oneoffs/carneiro/dataProcessing.scala b/scala/qscript/oneoffs/carneiro/dataProcessing.scala
index ae2ab4046..c9d03d5c3 100755
--- a/scala/qscript/oneoffs/carneiro/dataProcessing.scala
+++ b/scala/qscript/oneoffs/carneiro/dataProcessing.scala
@@ -72,6 +72,7 @@ class dataProcessing extends QScript {
 
     // BAM files generated by the pipeline
     val bamList: String         = outDir + outName + ".list"
+    val joinedBams: String      = outDir + outName + ".join.bam"
     val cleanedBam: String      = outDir + outName + ".clean.bam"
     val fixedBam: String        = outDir + outName + ".processed.bam"
 
@@ -119,8 +120,9 @@ class dataProcessing extends QScript {
 
 
     add(new writeList(recalibratedBamList, bamList),
-        new allTargets(bamList, allTargetIntervals),
-        new clean(bamList, allTargetIntervals, cleanedBam, !knownsOnly, !intermediate))
+        new joinBams(bamList, joinedBams),
+        new allTargets(joinedBams, allTargetIntervals),
+        new clean(joinedBams, allTargetIntervals, cleanedBam, !knownsOnly, !intermediate))
   }
 
   class TargetBase (outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
@@ -137,6 +139,7 @@ class dataProcessing extends QScript {
 
   class allTargets (inBams: String, outIntervals: String) extends TargetBase(outIntervals) {
       this.input_file :+= new File(inBams)
+      this.memoryLimit = Some(6)
       this.jobName = queueLogDir + outIntervals + ".atarget"
   }
 
@@ -199,8 +202,14 @@ class dataProcessing extends QScript {
   }
 
   class writeList(inBams: List[File], outBamList: String) extends ListWriterFunction {
-    this.inputFiles = inBams
-    this.listFile = new File(outBamList)
-    this.jobName = queueLogDir + outBamList + ".bamList"
+  this.inputFiles = inBams
+  this.listFile = new File(outBamList)
+  this.jobName = queueLogDir + outBamList + ".bamList"
+  }
+
+  class joinBams(inBams: File, outBam: String) extends PrintReads {
+  this.input_file :+= inBams
+  this.out = new File(outBam)
+  this.jobName = queueLogDir + inBams + ".joinBams"
   }
 }