diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
index 1ccaf687bb87e8843b5bf5140032d298867bb978..ea22e61d276012a64d87f7c24f9a02282b3bf8ca 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
@@ -36,6 +36,13 @@ class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction
 }
 
 object MergeAlleles extends ToolCommand {
+  def apply(root: Configurable, input: List[File], output: File): MergeAlleles = {
+    val mergeAlleles = new MergeAlleles(root)
+    mergeAlleles.input = input
+    mergeAlleles.output = output
+    return mergeAlleles
+  }
+
   case class Args(inputFiles: List[File] = Nil, outputFile: File = null, reference: File = null) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {