gnomad_toolbox.filtering.frequency

Functions for filtering the gnomAD sites HT frequency data.

Module Functions

`gnomad_toolbox.filtering.frequency.get_ancestry_callstats`(...)	Extract callstats for specified ancestry group(s).
`gnomad_toolbox.filtering.frequency.get_single_variant_ancestry_callstats`(...)	Extract callstats for specified ancestry group(s) and a single variant.

Functions for filtering the gnomAD sites HT frequency data.

gnomad_toolbox.filtering.frequency.get_ancestry_callstats(gen_ancs, **kwargs)[source]

Extract callstats for specified ancestry group(s).

Parameters:

gen_ancs (Union[str, List[str]]) – Genetic ancestry group(s) (e.g., ‘afr’, ‘amr’, ‘asj’, ‘eas’, ‘fin’, ‘nfe’, ‘oth’, ‘sas’). Can be a single ancestry group or a list of ancestry groups.
kwargs – Keyword arguments to pass to _get_dataset.

Return type:

Table

Returns:

Table with callstats for the given ancestry groups and variant.

gnomad_toolbox.filtering.frequency.get_single_variant_ancestry_callstats(gen_ancs, **kwargs)[source]

Extract callstats for specified ancestry group(s) and a single variant.

Parameters:

gen_ancs (Union[str, List[str]]) – Genetic ancestry group(s) (e.g., ‘afr’, ‘amr’, ‘asj’, ‘eas’, ‘fin’, ‘nfe’, ‘oth’, ‘sas’). Can be a single ancestry group or a list of ancestry groups.
kwargs – Keyword arguments to pass to get_single_variant.

Return type:

Table

Returns:

Table with callstats for the given ancestry groups and variant.