Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

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

rfarrerrfarrer Cambridge MAPosts: 11Member

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

Sign In or Register to comment.