Zarr VCF

[sounkou-bioinfo]

Hi all,

Thank you for this great work !

My question is with regard to the zarr vcf specs and the published paper https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giaf049/8154315. Are they any plans to support this or guidance on how to go about doing this ? I think this might be a worthwhile R Consortium grant project (or the topics of genomics ETL in general with zarr)

Best

[Bisaloo]

Hi @sounkou-bioinfo, thanks for getting in touch!

For my own reference, the detailed spec is here: https://github.com/sgkit-dev/vcf-zarr-spec/blob/main/vcf_zarr_spec.md

As far as I can tell, it should indeed be possible to build a package that depends on Rarr and implements this specification. It's a zarr store, and Rarr can read each individual array component.

The package would mostly need to link the information between the different arrays.

I don't have this in my immediate priority list but it could change in the future depending on the community adoption of this new format. In all cases, I'm also very happy to support any external effort towards this implementation.

[sounkou-bioinfo]

Thank you for your response @Bisaloo
My question is, if i were to make a package that depends on Rarr for this task, would it be more advisable to to this at the R or C Level, and if it is at the C level, it would be great if Rarr provided a linkingTo mechanism

[Bisaloo]

I don't think there is any need to interact with the C code, or even any deep internals from Rarr.

Everything related to Zarr reading should be handled out of the box by Rarr::read_zarr_array(). But the Zarr-VCF specs consists of multiple Zarr arrays, each containing a different piece of information.

The job of the Zarr-VCF wrapper would be to pull the information from the various arrays together. But once they are read, this is mostly R array manipulation: subsetting, merging, etc. some arrays / data.frames.

This is all based from my surface understanding of the Zarr-VCF format so I may be misunderstanding something.