sgkit.io.vcf.zarr_to_vcf

sgkit.io.vcf.zarr_to_vcf(input, output, *, vcf_header=None)

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.

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.

vcf_header : str | NoneOptional[str] (default: None)

The VCF header to use (including the line starting with #CHROM). If None, then a header will be generated from the dataset vcf_header attribute (if present), or from scratch otherwise.

Return type

None