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.
Non-model organism sub-forum?
I was wondering if perhaps there should be a sub-forum or some other such area dedicated to work on non-model organism?
Those of us working on non-model organisms (or even just non-human/mouse) face quite a few issues which folks working on humans don't. There are also a lot of (sophisticated) workflows, optimizations, and even terms which are used with human data which just don't apply to other organisms (except maybe mouse models).
It really boils down to: "Do you have a very good reference sequence and lots of annotations, or not".
Some of the topics would include:
- Pretty much everything when your population has a lot of variation (relative to humans at least)
- Variant calling with different ploidy (thankfully HC can now do)
- Reference-free methods
- What I'll call 'reference-lite' methods, where the reference is a guide but not really trusted
- Detecting and dealing with reference errors (gaps, chimeras, misassembly, ect.)
- Detecting big structural variants (eventually GenomeSTRiP should help)
Anyways, just an idea. I'm curious if there is enough interest in expanding the GATK toolset and best-practices to be more useful for non-model organisms.