Commit 046d7d2b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding exac annotation step

parent 4459b837
......@@ -56,17 +56,36 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
normalizer.outputVcf = swapExt(outputDir, vep.output, ".vcf", ".normalized.vcf.gz")
add(normalizer)
// Optional annotation steps, depend is some files existing in the config
val gonlVcfFile: Option[File] = config("gonl_vcf")
val exacVcfFile: Option[File] = config("exac_vcf")
var outputFile = normalizer.outputVcf
gonlVcfFile match {
case Some(gonlVcfFile) => {
val vcfWithVcf = new VcfWithVcf(this)
vcfWithVcf.input = normalizer.outputVcf
vcfWithVcf.input = outputFile
vcfWithVcf.secondaryVcf = gonlVcfFile
vcfWithVcf.output = swapExt(outputDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
add(vcfWithVcf)
outputFile = vcfWithVcf.output
}
case _ =>
}
exacVcfFile match {
case Some(exacVcfFile) => {
val vcfWithVcf = new VcfWithVcf(this)
vcfWithVcf.input = outputFile
vcfWithVcf.secondaryVcf = exacVcfFile
vcfWithVcf.output = swapExt(outputDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
vcfWithVcf.fields ::= ("MAF", "MAF_exac", None)
add(vcfWithVcf)
outputFile = vcfWithVcf.output
}
case _ => normalizer.outputVcf
case _ =>
}
}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment