Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

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

Sign In or Register to comment.