Commit 779e8aa3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed bcftools merge step

parent 9156f68c
......@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsCall, BcftoolsMerge }
import nl.lumc.sasc.biopet.extensions.gatk.{ GenotypeConcordance, CombineVariants }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
import nl.lumc.sasc.biopet.extensions.{ Ln, Bgzip, Tabix }
import nl.lumc.sasc.biopet.utils.Logging
import org.broadinstitute.gatk.utils.commandline.Input
......@@ -224,11 +224,13 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
bt.output
}
val bcfmerge = new BcftoolsMerge(qscript)
bcfmerge.input = sampleVcfs
bcfmerge.output = outputFile
bcfmerge.O = Some("z")
add(bcfmerge)
if (sampleVcfs.size > 1) {
val bcfmerge = new BcftoolsMerge(qscript)
bcfmerge.input = sampleVcfs
bcfmerge.output = outputFile
bcfmerge.O = Some("z")
add(bcfmerge)
} else add(Ln.apply(qscript, sampleVcfs.head, outputFile))
add(Tabix(qscript, outputFile))
}
}
......
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