diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index 56e2ddebb..56f6460fb 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -347,6 +347,7 @@ class DataProcessingPipeline extends QScript {
     this.knownSites ++= qscript.dbSNP
     this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
     this.input_file :+= inBam
+    this.disable_indel_quals = true
     this.out = outRecalFile
     if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform
     if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString)
@@ -359,7 +360,6 @@ class DataProcessingPipeline extends QScript {
   case class recal (inBam: File, inRecalFile: File, outBam: File) extends PrintReads with CommandLineGATKArgs {
     this.input_file :+= inBam
     this.BQSR = inRecalFile
-    this.disable_indel_quals = true
     this.baq = CalculationMode.CALCULATE_AS_NECESSARY
     this.out = outBam
     if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString)
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
index b7246ca8f..a4a6636fe 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
@@ -166,6 +166,7 @@ class PacbioProcessingPipeline extends QScript {
     this.knownSites :+= dbSNP
     this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
     this.input_file :+= inBam
+    this.disable_indel_quals = true
     this.out = outRecalFile
     this.analysisName = queueLogDir + outRecalFile + ".covariates"
     this.jobName = queueLogDir + outRecalFile + ".covariates"
@@ -178,7 +179,6 @@ class PacbioProcessingPipeline extends QScript {
     this.input_file :+= inBam
     this.BQSR = inRecalFile
     this.out = outBam
-    this.disable_indel_quals = true
     this.isIntermediate = false
     this.analysisName = queueLogDir + outBam + ".recalibration"
     this.jobName = queueLogDir + outBam + ".recalibration"