diff --git a/gatk.wdl b/gatk.wdl
index c100b461982af69b4f94ca587bc39d84163ab6ca..d94a4d26e5e379b19898a71db0a2d23ef04b6a96 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -442,6 +442,7 @@ task FilterMutectCalls {
 
     command {
         set -e
+        mkdir -p $(dirname ~{outputVcf})
         gatk --java-options -Xmx~{memory}G \
         FilterMutectCalls \
         -R ~{referenceFasta} \