gnomad_qc.v5.resources.annotations
Script containing annotation related resources.
Module Functions
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Get the downsampling annotation table. |
Get the group membership Table for coverage, AN, quality histograms, and frequency calculations. |
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Get the quality histograms annotation table. |
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Fetch filepath for all sites coverage or allele number Table. |
Script containing annotation related resources.
- gnomad_qc.v5.resources.annotations.get_aou_downsampling(test=False)[source]
Get the downsampling annotation table.
v5 downsamplings only applies to the AoU dataset.
- Parameters:
test (
bool) – Whether to use a tmp path for tests. Default is False.- Return type:
VersionedTableResource- Returns:
Hail Table containing downsampling annotations.
- gnomad_qc.v5.resources.annotations.group_membership(test=False, data_set='aou')[source]
Get the group membership Table for coverage, AN, quality histograms, and frequency calculations.
- Parameters:
test (
bool) – Whether to use a tmp path for tests. Default is False.data_set (
str) – Data set of annotation resource. Default is “aou”.
- Return type:
VersionedTableResource- Returns:
Hail Table containing group membership annotations.
- gnomad_qc.v5.resources.annotations.qual_hists(test=False)[source]
Get the quality histograms annotation table.
- Parameters:
test (
bool) – Whether to use a tmp path for tests. Default is False.- Return type:
VersionedTableResource- Returns:
Hail Table containing quality histogram annotations.
- gnomad_qc.v5.resources.annotations.coverage_and_an_path(test=False, data_set='aou')[source]
Fetch filepath for all sites coverage or allele number Table.
Note
If data_set is ‘gnomAD’, the returned table only contains coverage and AN for consent drop samples.
- Parameters:
test (
bool) – Whether to use a tmp path for testing. Default is False.data_set (
str) – Dataset identifier. Must be one of “aou” or “gnomad”. Default is “aou”.
- Return type:
VersionedTableResource- Returns:
Coverage and allele number Hail Table.