Commit 9a25fc2b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added stand_call_conf and stand_emit_conf option

parent 1df0bfa4
......@@ -57,6 +57,13 @@ class GatkGenotyping(val root:Configurable) extends QScript with BiopetQScript {
if (configContains("dbsnp")) this.dbsnp = config("dbsnp")
if (configContains("scattercount", "genotypegvcfs")) this.scatterCount = config("scattercount", 1, "genotypegvcfs")
this.out = outputFile
if (config("inputtype", "dna") == "rna") {
this.stand_call_conf = config("stand_call_conf", 20, "haplotypecaller")
this.stand_emit_conf = config("stand_emit_conf", 20, "haplotypecaller")
} else {
this.stand_call_conf = config("stand_call_conf", 30, "haplotypecaller")
this.stand_emit_conf = config("stand_emit_conf", 30, "haplotypecaller")
}
}
add(genotypeGVCFs)
return genotypeGVCFs.out
......
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