Commit bb46c239 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

changes to get rid of reference calls

parent 59923a55
......@@ -60,14 +60,11 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
sampleVcf
}
if (sampleVcfs.size > 1) {
val cv = new CombineVariants(this)
cv.inputFiles = sampleVcfs
cv.outputFile = outputFile
cv.setKey = "null"
cv.excludeNonVariants = true
add(cv)
} else add(Ln.apply(this, sampleVcfs.head, outputFile))
add(Tabix(this, outputFile))
val cv = new CombineVariants(this)
cv.inputFiles = sampleVcfs
cv.outputFile = outputFile
cv.setKey = "null"
cv.excludeNonVariants = true
add(cv)
}
}
Supports Markdown
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