sgkit.io.vcf.vcf_to_zarrs

sgkit.io.vcf.vcf_to_zarrs(input, output, regions, chunk_length=10000, chunk_width=1000, output_storage_options=None, ploidy=2, mixed_ploidy=False, truncate_calls=False)

Convert VCF files to multiple Zarr on-disk stores, one per region.

Parameters

input : str, Path, Sequence[Union[str, Path]]Union[str, Path, Sequence[Union[str, Path]]]

A path (or paths) to the input BCF or VCF file (or files). VCF files should be compressed and have a .tbi or .csi index file. BCF files should have a .csi index file.

output : str, PathUnion[str, Path]

Path to directory containing the multiple Zarr output stores.

regions : None, Sequence[str], Sequence[Optional[Sequence[str]]]Union[None, Sequence[str], Sequence[Optional[Sequence[str]]]]

Genomic region or regions to extract variants for. For multiple inputs, multiple input regions are specified as a sequence of values which may be None, or a sequence of region strings.

chunk_length : intint (default: 10000)

Length (number of variants) of chunks in which data are stored, by default 10,000.

chunk_width : intint (default: 1000)

Width (number of samples) to use when storing chunks in output, by default 1,000.

output_storage_options : {str: str}, NoneOptional[Dict[str, str]] (default: None)

Any additional parameters for the storage backend, for the output (see fsspec.open).

ploidy : intint (default: 2)

The (maximum) ploidy of genotypes in the VCF file.

mixed_ploidy : boolbool (default: False)

If True, genotype calls with fewer alleles than the specified ploidy will be padded with the non-allele sentinel value of -2. If false, calls with fewer alleles than the specified ploidy will be treated as incomplete and will be padded with the missing-allele sentinel value of -1.

truncate_calls : boolbool (default: False)

If True, genotype calls with more alleles than the specified (maximum) ploidy value will be truncated to size ploidy. If false, calls with more alleles than the specified ploidy will raise an exception.

Return type

Sequence[str]Sequence[str]

Returns

A list of URLs to the Zarr outputs.