The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
Register now for the upcoming GATK Best Practices workshop, Nov 7-8 at the Broad in Cambridge, MA. Open to all comers! More info and signup at

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

rfarrerrfarrer Cambridge MAPosts: 13Member

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.


Best Answer


  • rfarrerrfarrer Cambridge MAPosts: 13Member

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

  • pdexheimerpdexheimer Posts: 543Member, Dev ✭✭✭✭

    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

Sign In or Register to comment.