diff --git a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
index 06ce05a00745fc1b71a30340d43b57284f0b4ab8..9ee6d59525af89650a5e4d4812ecdad5df4dee6c 100644
--- a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
+++ b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
@@ -98,7 +98,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
 
         val regionDir = new File(outputDir, "snptest" + File.separator + region.chr)
         val bedDir = new File(outputDir, ".queue" + File.separator + "regions" + File.separator + region.chr)
-        regionDir.mkdirs()
+        bedDir.mkdirs()
         val bedFile = new File(bedDir, s"${name}.bed")
         BedRecordList.fromList(List(region)).writeToFile(bedFile)
         bedFile.deleteOnExit()