malariagen_data.amin1.Amin1.snp_calls

Amin1.snp_calls(region, site_mask=False, inline_array=True, chunks='native')

Access SNP sites, site filters and genotype calls.

Parameters

region: str or list of str or Region

Contig (e.g., “KB663610”), gene name (e.g., “AMIN002150”), genomic region defined with coordinates (e.g., “KB663610:1-100000”) or a named tuple with genomic location Region(contig, start, end). Multiple values can be provided as a list, in which case data will be concatenated.

site_maskbool

Apply site filters.

inline_arraybool, optional

Passed through to dask.array.from_array().

chunksstr, optional

If ‘auto’ let dask decide chunk size. If ‘native’ use native zarr chunks. Also can be a target size, e.g., ‘200 MiB’.

Returns

ds : xarray.Dataset