diff --git a/build.xml b/build.xml
index 4e7c642ba..e18dfa8de 100644
--- a/build.xml
+++ b/build.xml
@@ -298,6 +298,13 @@
             <src path="${queue-extensions.source.dir}" />
             <include name="**/*.scala"/>
             <exclude name="**/gridengine/**" unless="include.gridengine" />
+            <!--
+            NOTE: Added include.queue.pipeline flag while VQSR v2 is being migrated
+            and the pipeline package is still using the old version.
+            At this moment enabling the flag turns on code that doesn't compile.
+            ASAP determine if package should use v2 or be retired.
+            -->
+            <exclude name="**/queue/pipeline/**" unless="include.queue.pipeline" />
         </scalac>
     </target>
 
diff --git a/scala/qscript/playground/FullCallingPipeline.q b/scala/qscript/playground/FullCallingPipeline.q
index 3f0e460fe..b6a14ce6f 100755
--- a/scala/qscript/playground/FullCallingPipeline.q
+++ b/scala/qscript/playground/FullCallingPipeline.q
@@ -94,6 +94,7 @@ class FullCallingPipeline extends QScript {
     indels.jobOutputFile = ".queue/logs/IndelCalling/UnifiedGenotyper.indels.out"
     indels.downsample_to_coverage = 600
     indels.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL
+    indels.GSA_PRODUCTION_ONLY = true /* use old indel genotyper */
     indels.input_file = List(writeBamList.listFile)
     indels.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
     indels.out = "IndelCalls/" + base+".indels.vcf"