gnomad_toolbox.load_data

Functions to import gnomAD data.

Module Functions

gnomad_toolbox.load_data.GnomADSession()	Class to manage the default data type and version for a gnomAD session.
gnomad_toolbox.load_data.get_gnomad_release([...])	Get gnomAD HT by dataset, data type, and version.
gnomad_toolbox.load_data.get_compatible_dataset_versions(dataset)	Get the compatible version of another datasets for a given gnomAD variant data version.

Functions to import gnomAD data.

class gnomad_toolbox.load_data.GnomADSession

Class to manage the default data type and version for a gnomAD session.

set_default_data(data_type=None, version=None)

Set default data type and version.

Parameters:

• data_type (Optional[str]) – Data type (exomes, genomes, or joint).

• version (Optional[str]) – gnomAD version.

Return type:

None

Returns:

None.

gnomad_toolbox.load_data.get_gnomad_release(dataset='variant', data_type=None, version=None)

Get gnomAD HT by dataset, data type, and version.

Not all combinations of dataset, data type, and version are available and/or supported by the toolbox. The table below shows what is supported.

Available versions for each dataset and data type are (as of 2025-1-13)

Genome Build	Dataset	Version	Data Types
GRCh37	variant	2.1.1	exomes, genomes
	coverage	2.1	exomes, genomes
	constraint	2.1.1	N/A
	pext	v7	base_level, annotation_level
	liftover	2.1.1	exomes, genomes
GRCh38	variant	4.1	exomes, genomes, joint
	all_sites_an	4.1	exomes, genomes
	browser	4.1	N/A (joint, but doesn’t need to be specified)
	coverage	3.0.1	genomes
	constraint	4.1	N/A
	pext	v10	base_level, annotation_level

Parameters:

• dataset (str) – Dataset type. One of “variant”, “coverage”, “all_sites_an”, “constraint”, “liftover”, “pext”, “browser”. Default is “variant”.

• data_type (Optional[str]) – Data type. One of “exomes”, “genomes”, “joint” for all datasets except “pext” where it is one of “base_level”, “annotation_level”. Default is the current session data type.

• version (Optional[str]) – gnomAD dataset version. Default is the current session version.

Return type:

Table

Returns:

Hail Table for requested dataset, data type, and version.

gnomad_toolbox.load_data.get_compatible_dataset_versions(dataset, variant_version=None, data_type=None)

Get the compatible version of another datasets for a given gnomAD variant data version.

Parameters:

• dataset (str) – Dataset to get the compatible version for.

• variant_version (Optional[str]) – Optional gnomAD variant data version. If not provided, the current session version is used.

• data_type (Optional[str]) – Optional data type for the dataset if applicable.

Return type:

Union[str, dict]

Returns:

Compatible version of the dataset for the given variant version.