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.
UnifiedGenotyper queue extension
It says in the "ExampleUnifiedGenotyper" qscript that it runs an incomplete version of the UnifiedGenotyper. I have a two questions about this.
- I cannot find the org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper class, is this not in the public source or am I blind?
- Does the "incomplete" in the script starting comment mean that this extension is incomplete in its functionality? Or is it something else that is incomplete in its nature?
Basically I'm wondering if there are any pitfalls for me if I start using the example script as a base for my own variant calling qscript.