sgkit.io.vcf.zarr_to_vcf

sgkit.io.vcf.zarr_to_vcf(input, output)

Convert a Zarr file to a VCF file.

A convenience for sgkit.load_dataset() followed by write_vcf().

Refer to write_vcf() for details and limitations.

Warning

This function requires the input Zarr file to have a vcf_header attribute containing the VCF header. VCF files converted to Zarr using vcf_to_zarr() will contain this attribute, but datasets loaded from other sources will not.

Parameters

input : str | Path | MutableMapping[str, bytes]Union[str, Path, MutableMapping[str, bytes]]

Zarr store or path to directory in file system.

output : str | Path | TextIOUnion[str, Path, TextIO]

A path or text file object that the output VCF should be written to.

Return type

None