bio2zarr

bio2zarr efficiently converts common bioinformatics formats to Zarr format.

Tools

• vcf2zarr converts VCF data to VCF Zarr format.

• plink2zarr converts PLINK 1.0 data to VCF Zarr format.

• tskit2zarr converts tskit data into VCF Zarr format.

• vcfpartition is a utility to split an input VCF into a given number of partitions. This is useful for parallel processing of VCF data.

Development status

bio2zarr is in development, contributions, feedback and issues are welcome at the GitHub repository.

If you would like to see support for other formats such as BGEN (or an interested in helping with implementing), please open an issue on Github to discuss!

Python APIs

There is access to some limited functionality via Python APIs (documented along with the respective tools). These are in beta, and should be fully documented and stabilised in the coming releases. General APIs to enable efficient and straightforward encoding of data to VCZ are planned (see issue #412).