diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
index 4578e32298b66cb76ee6e3e8b422626e18e73c25..75ba6c3ab2f74eec60d7854dcde064ad052f830b 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
@@ -42,19 +42,19 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
 
   @Test def testOutputTypeVcf() = {
     val tmp_path = "/tmp/VcfWithVcf_" + rand.nextString(10) + ".vcf"
-    val arguments = Array("-I", unvepped_path, "-S", vepped_path, "-O", tmp_path, "-f", "CSQ")
+    val arguments = Array("-I", unvepped_path, "-s", vepped_path, "-o", tmp_path, "-f", "CSQ")
     main(arguments)
   }
 
   @Test def testOutputTypeVcfGz() = {
     val tmp_path = "/tmp/VcfWithVcf_" + rand.nextString(10) + ".vcf.gz"
-    val arguments = Array("-I", unvepped_path, "-S", vepped_path, "-O", tmp_path, "-f", "CSQ")
+    val arguments = Array("-I", unvepped_path, "-s", vepped_path, "-o", tmp_path, "-f", "CSQ")
     main(arguments)
   }
 
   @Test def testOutputTypeBcf() = {
     val tmp_path = "/tmp/VcfWithVcf_" + rand.nextString(10) + ".bcf"
-    val arguments = Array("-I", unvepped_path, "-S", vepped_path, "-O", tmp_path, "-f", "CSQ")
+    val arguments = Array("-I", unvepped_path, "-s", vepped_path, "-o", tmp_path, "-f", "CSQ")
     main(arguments)
   }