diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
index db20cb677c82fd647c9b7827a23331fa8cc04ab7..389e118b873e551d15451988a20af8356883e4fa 100644
--- a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
+++ b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
@@ -111,6 +111,7 @@ class Gatk(private var globalConfig: Config) extends QScript {
         val catVariants = new CatVariants()
         catVariants.variant = Seq(snpApplyRecalibration.out,indelApplyRecalibration.out)
         catVariants.outputFile = swapExt(genotypeGVCFs.out,".vcf",".recal.vcf")
+        catVariants.reference = referenceFile
         add(catVariants)
       } else logger.warn("No gVCFs to genotype")