sgkit-dev / sgkit

Scalable genetics toolkit
https://sgkit-dev.github.io/sgkit
Apache License 2.0
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Document reading tabular pedigree formats into sgkit #1012

Open timothymillar opened 1 year ago

timothymillar commented 1 year ago

We don't currently have any IO functionality for pedigree formats. These are usually tabular but can be quite variable. We should document how to read in some generic examples and add them to an sgkit style dataset.

Basic workflow:

timothymillar commented 1 year ago

@jeromekelleher suggests also adding "Pedigree statistics" top level section to the documentation https://github.com/pystatgen/sgkit/issues/1025#issuecomment-1436755539.

I was actually just looking for documentation this morning answering a question about computing inbreeding from simulations

Could you give some more detail on these simulations?

jeromekelleher commented 1 year ago

Discussion here: https://github.com/tskit-dev/tskit/discussions/2711

timothymillar commented 1 year ago

This is mostly covered by #1072, but I might leave it open for now as I think there is room for more pedigree specific documentation.