diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala
index 2640c8f21224b7a504bb73c2a07c0e38e674fcbf..0a2e48c00688c6cf097066498cd4f6a62f54b107 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala
@@ -71,6 +71,7 @@ trait CufflinksProducer {
       job.input = alnFile
       job.library_type = Option(strandedness)
       job.output_dir = new File(sampleDir, name)
+      /*
       job.GTF = cuffType match {
         case CufflinksStrict => pipeline.annotationGtf
         case otherwise       => None
@@ -79,6 +80,7 @@ trait CufflinksProducer {
         case CufflinksGuided => pipeline.annotationGtf
         case otherwise       => None
       }
+      */
       job
     }