20250512 developer call notes

[tomwhite]

20250512

Pre-notes

• Notes from previous meeting

PRs

Issues

Discussions

• Release bio2zarr/vcztools following click 8.2.0 incompatibility
• Generalised filtering/retrieval in vcztools - next steps
• VCF Header work in bio2zarr/vcztools/spec

Notes

Attendees

1. Tom White
2. Jerome Kelleher
3. Ben Jeffery
4. Per Unneberg

Discussion

Paper

• JK: Proofs back from production. 200+ nitpicks to go through. Main thing we need from authors is addresses. Publicity - some are interested.

Click

• Mainly a moan about Python dependencies!
• JK: side note; GeL like containers - can we make Docker containers?
• PU: using Pixie for dependency resolution, sort of Conda replacement (not a container)
• JK: need a release of vcztools
• BJ: tskit doesn’t have a cli in bio2zarr, so easy to release now (but no rush on it)
• JK: keep other file formats optional
• TW: we should drop plink from sgkit when it’s supported in bio2zarr
• JK: plink and bgen could be left in sgkit - but at least give people a heads up
• TW: cycvf2 wheel build is broken
• BJ: bgen priority?
• JK: fairly low, main reason is to simplify sgkit - TW can do if it helps

Vcztools

• TW: Retrieval is much improved now. I can look at some of the filter options
• JK: FILTER field, variables (NPASS etc), functions. See https://github.com/browning-lab/ukb-phasing/blob/master/phase.ukb
• TW: sgkit integration - 1. Filtering language, 2. Dataset to vcf or query format
  • See How to make a small zarr file from a large VCF? bio2zarr#365 for 1