diff --git a/scala/qscript/playground/HybridSelectionPipeline.scala b/scala/qscript/playground/HybridSelectionPipeline.scala
index 6bb9b4eb7..64d50bbf2 100755
--- a/scala/qscript/playground/HybridSelectionPipeline.scala
+++ b/scala/qscript/playground/HybridSelectionPipeline.scala
@@ -134,7 +134,7 @@ class HybridSelectionPipeline extends QScript {
     combineSNPsIndels.rodBind :+= RodBind("indels", "VCF", filterIndels.out)
     combineSNPsIndels.rodBind :+= RodBind("snps", "VCF", filterSNPs.out)
     combineSNPsIndels.rod_priority_list = "indels,snps"
-    combineSNPsIndels.filteredRecordsMergeType = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.UNION
+    combineSNPsIndels.filteredRecordsMergeType = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED
     combineSNPsIndels.assumeIdenticalSamples = true
     combineSNPsIndels.out = projectBase + ".unannotated.vcf"
     combineSNPsIndels.jobOutputFile = combineSNPsIndels.out + ".out"
diff --git a/scala/qscript/playground/WholeGenomePipeline.scala b/scala/qscript/playground/WholeGenomePipeline.scala
index 0d0ebbf60..d8584a800 100644
--- a/scala/qscript/playground/WholeGenomePipeline.scala
+++ b/scala/qscript/playground/WholeGenomePipeline.scala
@@ -158,7 +158,7 @@ class WholeGenomePipeline extends QScript {
     val combineChunks = new CombineVariants with CommandLineGATKArgs
     combineChunks.rodBind = chunkVcfs.zipWithIndex.map { case (vcf, index) => RodBind("input"+index, "VCF", vcf) }
     combineChunks.rod_priority_list = chunkVcfs.zipWithIndex.map { case (vcf, index) => "input"+index }.mkString(",")
-    combineChunks.filteredRecordsMergeType = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.UNION
+    combineChunks.filteredRecordsMergeType = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED
     combineChunks.assumeIdenticalSamples = true
     combineChunks.out = projectBase + ".unfiltered.vcf"
     combineChunks.jobOutputFile = combineChunks.out + ".out"