From a6e9c46981903c22bf78308435ed6a5b5068795f Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Mon, 12 Oct 2015 13:15:57 +0200
Subject: [PATCH] mpileup_reference_added

---
 .../sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala  | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
index 26302af07..3adcbbf5e 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
@@ -161,6 +161,8 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
       val mp = new SamtoolsMpileup(qscript)
       mp.input = inputBams
       mp.u = true
+      //TODO: proper piping should be implemented
+      mp.reference = referenceFasta()
 
       val bt = new BcftoolsCall(qscript)
       bt.O = "z"
-- 
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