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Commit fb53f990 authored by Peter van 't Hof's avatar Peter van 't Hof
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added bgzip and tabix to freebayes

parent e12f0f66
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...@@ -4,7 +4,7 @@ import java.io.File ...@@ -4,7 +4,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, SampleLibraryTag } import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.summary.SummaryQScript import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.Gzip import nl.lumc.sasc.biopet.extensions.{ Tabix, Bgzip, Gzip }
import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsCall import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsCall
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
...@@ -92,13 +92,24 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag { ...@@ -92,13 +92,24 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
val name = "freebayes" val name = "freebayes"
protected val defaultPrio = 7 protected val defaultPrio = 7
def outputFile = new File(outputDir, namePrefix + ".freebayes.vcf") def outputFile = new File(outputDir, namePrefix + ".freebayes.vcf.gz")
def addJobs() { def addJobs() {
val fb = new nl.lumc.sasc.biopet.extensions.Freebayes(qscript) val fb = new nl.lumc.sasc.biopet.extensions.Freebayes(qscript)
fb.bamfiles = inputBams fb.bamfiles = inputBams
fb.outputVcf = outputFile fb.outputVcf = new File(outputDir, namePrefix + ".freebayes.vcf")
fb.isIntermediate = true
add(fb) add(fb)
val bz = new Bgzip(qscript)
bz.input = List(fb.outputVcf)
bz.output = outputFile
add(bz)
val ti = new Tabix(qscript)
ti.input = bz.output
ti.p = Some("vcf")
add(ti)
} }
} }
......
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