Starting this issue as catch-all for lower priority, longer term tasks.
Containerization would probably be a useful long-term goal and is probably not too difficult considering that everything is already highly conda-ized.
Add profiles for other queuing software, e.g. LSF? This will make everything much more broadly useful to a wider community.
Deal with variant filtering in a more robust way
Add variation annotation with SnpEff
Consider adding more variant callers (e.g. FreeBayes, samtools), and especially new(ish) ones like Octopus, Varlociraptor, DeepVariant, although many of the newer variant callers are even more tuned for humans than GATK
Add more downstrem analysis options. Most of these would need to be optional modules and probably would be better off in a separate repository, as few users would want to run everything. But, adding in e.g. MK work or integration with ANGSD could have value.
Handle sex chromosomes appropriately where known; identify sex chromosomes where unknown but sex of individuals is known?
Integrate a tool like pseudo-it to improve cross-species mapping
Consider transfering repository to an organization if we intend to add more downstream analysis or use Github for additional related projects (e.g., additional code for first paper).
Starting this issue as catch-all for lower priority, longer term tasks.