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