diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
index 0eccb89d19bb746f826c8d73e99da7da2bbd6859..fd5b06cd4e62719255a5c6a761807d08525cd7a1 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
@@ -36,6 +36,7 @@ class Delly(val root: Configurable) extends SvCaller {
       val catVariants = new CatVariants(this)
       catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf")
       catVariants.isIntermediate = true
+      catVariants.writeHeaderToEmptyOutput = true
 
       if (del) {
         val delly = new DellyCaller(this)