diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 96051dc4a24f5db151bf78cc3b9f3b280b93025e..b016e17dc071f4a7704334bc5f81882263e2ceba 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -135,7 +135,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
       mergBuffer += ("9.raw" -> scriptOutput.rawFilterVcfFile)
 
       if (useAllelesOption.get) {
-        val mergeAlleles = MergeAlleles(this, mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz.tbi")
+        val mergeAlleles = MergeAlleles(this, mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz")
         add(mergeAlleles, isIntermediate = true)
 
         if (useHaplotypecaller.get) {