diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index 578f3afc79f6cac8d2621399bb577222383ee2bb..19973c3e1fdc030daecbfbc3ac7d6125bd9c4f04 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -38,7 +38,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
   def this() = this(null)
 
   override def defaults = ConfigUtils.mergeMaps(Map(
-    "mapping" -> Map("skip_markduplicates" -> true)
+    "mapping" -> Map("skip_markduplicates" -> true, "aligner" -> "bwa")
   ), super.defaults)
 
   def makeSample(id: String) = new Sample(id)