Commit a6e9c469 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

mpileup_reference_added

parent 98bc93d9
......@@ -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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