Jerome Kelleher comments

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                                            Jerome Kelleher

Unused alleles being `""` is confusing for downstream tools - consider `None`?

Good question - maybe it's something to do with ragged multi-character alleles (e.g. indels)?

Wouldn't use module zip file

Thanks, that seems to be working quite well now.

Wouldn't use module zip file

It's actually chugging away pretty well, so I'm going to leave it.

sgkit.io.vcf.vcf_to_zarr() fails to convert VCFs with INFO/CSQ and other unbounded annotations

Good questions @tnguyengel! Any thoughts @tomwhite?

Add folder structure for documents

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

Populate parent_id variable in `read_plink`

Need to be careful about potential zero and one-based differences here. What do we currently do with plink-like pedigrees @timothymillar ?

Example notebook exercising pairwise distance on GPU

Thanks @aktech, I'll be in touch!

Write family information in `write_plink`

This is tricky, I don't think we thought much about interoperability with Plink when doing the pedigree encoding @timothymillar ?

tskit example of sgkit Zarr for intermediate data

The point we're illustrating here is the power of open and extensible formats. Previously we had to convert VCFs to our own zarr formats which was time-consuming and tedious. Now...

maximise lossless compression of vcf_to_zarr

Have you got an example where the we don't do so well on compression @elswob? I'm guessing it's some particular INFO or FORMAT field that's not being dealt with well.