diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index 7d8a04d4f01223a894954bc61a6cd3f477371b5d..5e80f114c82bd16fb1efd7788158f31d1c2c0f05 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -144,8 +144,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
             config("bam_to_fastq", default = false).asBoolean match {
               case true =>
                 val samToFastq = SamToFastq(qscript, config("bam"),
-                  new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
-                  new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
+                  new File(libDir, sampleId + "-" + libId + ".R1.fq.gz"),
+                  new File(libDir, sampleId + "-" + libId + ".R2.fq.gz"))
                 samToFastq.isIntermediate = true
                 qscript.add(samToFastq)
                 mapping.foreach(mapping => {