20240916 developer call notes #1260

tomwhite · 2024-09-16T16:08:41Z

tomwhite
Sep 16, 2024
Maintainer

JK: OFH hackathon
- 5M people’s genomes + health records
- Using simulated data from paper on Azure
- Perf was generally good running vcztools and afdist clone
- Idea of how to use a Zarr store for variants
- Add Azure benchmarks to paper
TW: meeting with GATK team
- Interested in adding Zarr VCF to htsjdk
- Would most naturally fit with export from Genomic Variant Store (GVS), used for All Of Us project
- Invited JK to give a talk about VCF Zarr
- JH: contact Zarr folks about Java status
- JK: would be good to turn up to meeting with a few lines of code that show how to read VCZ from Java
SAIGE
- WT: Got Tensorstore working finally by making it a dynamic library.
- WT: Can focus on code now.
- WT: Reading variant by variant should be straightforward
- JK: Talk to users - how to turn into something people use
- JH: if we get it working we tell people via the paper
Tensorstore
- JH: had a call with TS manager. Main dev is Jeremy (JMS) (and Laramie). Three main user communities: connectomics, Gemini (JAX, optax), everyone else. Sits within Google Research - Science AI. Zarr has a “small files problems” - OCDBT. TLDR: JMS is the person to talk to.
- JK: we want to add TS to benchmarks in paper - good for science results. Blocked on the hardware issue, so need to bump this.
Cubed + sgkit
- QC pipeline is basically working
- JK: maybe for GEL aggv4?
- TW: next JAX experiment; linalg (QR, SVD, PCA) to support GWAS