diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
index 678b356ee..51de3a7ad 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
@@ -41,9 +41,9 @@ class RecalibrateBaseQualities extends QScript {
 
     nContigs = getNumberOfContigs(input)
 
-    val recalFile1: File = new File("recal1.csv")
-    val recalFile2: File = new File("recal2.csv")
-    val recalBam: File        = swapExt(input, ".bam", "recal.bam")
+    val recalFile1: File = swapExt(input, ".bam", "recal1.csv")
+    val recalFile2: File = swapExt(input, ".bam", "recal2.csv")
+    val recalBam: File   = swapExt(input, ".bam", "recal.bam")
     val path1: String    = "before"
     val path2: String    = "after"
     
@@ -88,4 +88,4 @@ class RecalibrateBaseQualities extends QScript {
     this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
     this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
   }
-}
\ No newline at end of file
+}