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

rfarrerrfarrer Cambridge MAMember

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

Best Answer

Answers

  • rfarrerrfarrer Cambridge MAMember

    It's worked! Brilliant. Thanks. I just added "genotyper.ploidy = 1"

  • pdexheimerpdexheimer Member ✭✭✭✭

    For anyone finding this thread later on - it doesn't matter which form of the argument you use in Queue (long or short). Either will work

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