malariagen_data.af1.Af1.snp_genotypes

Af1.snp_genotypes(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, sample_indices: List[int] | None = None, field: str = 'GT', site_mask: str | None = None, inline_array: bool = True, chunks: str | Tuple[int, ...] = 'native') → Array

Access SNP genotypes and associated data.

Parameters

regionstr or Region or Mapping or list of str or Region or Mapping or tuple of str or Region or Mapping

Region of the reference genome. Can be a contig name, region string (formatted like “{contig}:{start}-{end}”), or identifier of a genome feature such as a gene or transcript. Can also be a sequence (e.g., list) of regions.

sample_setssequence of str or str or None, optional

List of sample sets and/or releases. Can also be a single sample set or release.

sample_querystr or None, optional

A pandas query string to be evaluated against the sample metadata, to select samples to be included in the returned data.

sample_indiceslist of int or None, optional

Advanced usage parameter. A list of indices of samples to select, corresponding to the order in which the samples are found within the sample metadata. Either provide this parameter or sample_query, not both.

fieldstr, optional, default: ‘GT’

Name of array or column to access.

site_maskstr or None, optional

Which site filters mask to apply. See the site_mask_ids property for available values.

inline_arraybool, optional, default: True

Passed through to dask from_array().

chunksstr or tuple of int, optional, default: ‘native’

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

Returns

Array

An array of either genotypes (GT), genotype quality (GQ), allele depths (AD) or mapping quality (MQ) values.