Projects that could use sgkit

[hammer]

I'd like to track some repos that might benefit or benefit from sgkit. If they're doing population or statistical genetics in Python, drop it here!

[hammer]

• https://github.com/hringbauer/hapROH
• https://github.com/jeremymcrae/liftover
• https://github.com/jeremymcrae/ld_estimator
• https://github.com/nadavbra/pwas
• https://github.com/popgenmethods/pyrho

[alimanfoo]

I'll add this one - https://github.com/malariagen/vector-data - which has the notebooks backing the MalariaGEN vector data user guide - https://malariagen.github.io/vector-data/landing-page.html. Ultimately it would be great to migrate all of the notebooks to use sgkit instead of scikit-allel.

[jeromekelleher]

This is the one I'm most interested in: https://github.com/tskit-dev/tsinfer

Currently tsinfer uses a custom wrapper around zarr, and users have to manually import their data manually. The plan is to remove this layer entirely, and to instead depend on sgkit datasets with the required variables.