how do i set the ploidy flag in a scala script?

rfarrerrfarrer Cambridge MAPosts: 12Member

Hi all, I am running a scala script, and would like to the include "-ploidy 1". Any advice on how can I do this?

Some information that may or may not be relevant (idk!):

I am attempting this using UnifiedGenotyper (v2.7-4). At the top of the script I have: package org.broadinstitute.sting.queue.qscripts.examples import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.extensions.gatk._

I got the glm both to work using: genotyper.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH

I was hoping for something similar for ploidy.

Thanks, Rhys

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