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.