Commit 4459b837 authored by Peter van 't Hof's avatar Peter van 't Hof

Adding gonl annotation step

parent 61926852
......@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, Reference }
import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
import nl.lumc.sasc.biopet.tools.VepNormalizer
import nl.lumc.sasc.biopet.tools.{ VcfWithVcf, VepNormalizer }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
......@@ -53,8 +53,21 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val normalizer = new VepNormalizer(this)
normalizer.inputVCF = vep.output
normalizer.outputVCF = swapExt(vep.output, ".vcf", ".normalized.vcf.gz")
normalizer.outputVcf = swapExt(outputDir, vep.output, ".vcf", ".normalized.vcf.gz")
add(normalizer)
val gonlVcfFile: Option[File] = config("gonl_vcf")
gonlVcfFile match {
case Some(gonlVcfFile) => {
val vcfWithVcf = new VcfWithVcf(this)
vcfWithVcf.input = normalizer.outputVcf
vcfWithVcf.secondaryVcf = gonlVcfFile
vcfWithVcf.output = swapExt(outputDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
add(vcfWithVcf)
}
case _ => normalizer.outputVcf
}
}
def summaryFile = new File(outputDir, "Toucan.summary.json")
......
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