sgkit.read_vcfzarr

sgkit.read_vcfzarr(path)

Read a VCF Zarr file created using scikit-allel.

Loads VCF variant, sample, and genotype data as Dask arrays within a Dataset from a Zarr file created using scikit-allel’s vcf_to_zarr function.

Since vcf_to_zarr does not preserve phasing information, there is no sgkit.variables.call_genotype_phased_spec variable in the resulting dataset.

Parameters

path : str, PathUnion[str, Path]

Path to the Zarr file.

Return type

DatasetDataset

Returns

A dataset containing the following variables:

• sgkit.variables.variant_id_spec (variants)

• sgkit.variables.variant_contig_spec (variants)

• sgkit.variables.variant_position_spec (variants)

• sgkit.variables.variant_allele_spec (variants)

• sgkit.variables.sample_id_spec (samples)

• sgkit.variables.call_genotype_spec (variants, samples, ploidy)

• sgkit.variables.call_genotype_mask_spec (variants, samples, ploidy)