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SGKit has (at least one) xarray datasets to simplify API creation for variant calling datasets.
I'm creating a documentation PR in order to understand the xarray dataset created by sgkit.api.create_genotype_call_dataset .
This will be broken down into 3 parts:
Minimal example using just straight numpy arrays with pictures.
Example reading in from a VCF. This will be with the understanding that this is for conceptual understanding only, and vcfs should be converted using the vcf_to_zarr function.
Full example using the Malaria Phase 2 datasets already preprocessed to zarr.