Sgkit is a Python package that provides a variety of analytical genetics methods through the use of general-purpose frameworks such as Xarray, Pandas, Dask and Zarr.
For more information on using sgkit, see the documentation.
Genetic file conversion: Use bio2zarr
to convert genetic file formats to Zarr, then load them with sgkit.load_dataset.
The BGEN reader, conversion functions and bgen extra have been removed;
sgkit no longer depends on cbgen. Use a bio2zarr version with BGEN support
(tracked in bio2zarr issue 417).
See the BGEN migration guide for details and
unpack_variables, retained only for existing legacy packed Zarr stores.
The sgkit project uses a custom governance model and is fiscally sponsored by NumFOCUS. Consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
