gnomad_qc.v5.resources.annotations

Script containing annotation related resources.

Module Functions

`gnomad_qc.v5.resources.annotations.get_trio_stats`([...])	Get gnomAD v5 (AoU genomes only) trio stats VersionedTableResource.
`gnomad_qc.v5.resources.annotations.get_sib_stats`([...])	Get the gnomAD v5 (AoU genomes only) sibling stats VersionedTableResource.
`gnomad_qc.v5.resources.annotations.get_aou_downsampling`([...])	Get the downsampling annotation table.
`gnomad_qc.v5.resources.annotations.group_membership`([...])	Get the group membership Table for coverage, AN, quality histograms, and frequency calculations.
`gnomad_qc.v5.resources.annotations.qual_hists`([...])	Get the quality histograms annotation table.
`gnomad_qc.v5.resources.annotations.coverage_and_an_path`([...])	Fetch filepath for all sites coverage or allele number Table.
`gnomad_qc.v5.resources.annotations.get_freq`([...])	Get the frequency annotation Table for v5.
`gnomad_qc.v5.resources.annotations.get_info_ht`([...])	Get the gnomAD v5 (AoU genomes only) info VersionedTableResource.
`gnomad_qc.v5.resources.annotations.info_vcf_path`([...])	Path to sites VCF (input information for running VQSR).
`gnomad_qc.v5.resources.annotations.get_aou_vcf_header`([...])	Get path to AoU annotation sites-only VCF header.
`gnomad_qc.v5.resources.annotations.get_aou_annotated_sites_only_vcf`([...])	Get path to AoU sites-only VCF with annotations needed for variant QC.
`gnomad_qc.v5.resources.annotations.get_vep`([...])	Get the gnomAD v5 VEP annotation VersionedTableResource.
`gnomad_qc.v5.resources.annotations.validate_vep_path`([...])	Get the gnomAD v5 VEP annotation VersionedTableResource for validation counts.

Script containing annotation related resources.

gnomad_qc.v5.resources.annotations.get_trio_stats(test=False, environment='rwb')[source]

Get gnomAD v5 (AoU genomes only) trio stats VersionedTableResource.

Parameters:

test (bool) – Whether to use a temporary path for testing.
environment (str) – Environment to use. Default is “rwb”. Must be one of “rwb” or “batch”.

Return type:

VersionedTableResource

Returns:

AoU trio stats VersionedTableResource.

gnomad_qc.v5.resources.annotations.get_sib_stats(test=False, environment='rwb')[source]

Get the gnomAD v5 (AoU genomes only) sibling stats VersionedTableResource.

Parameters:

test (bool) – Whether to use a tmp path for testing.
environment (str) – Environment to use. Default is “rwb”. Must be one of “rwb” or “batch”.

Return type:

VersionedTableResource

Returns:

AoU sibling stats VersionedTableResource.

gnomad_qc.v5.resources.annotations.get_aou_downsampling(test=False, environment='rwb')[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.
environment (str) – Environment to use. Default is “rwb”. Must be one of “rwb” or “batch”.

Return type:

VersionedTableResource

Returns:

Hail Table containing downsampling annotations.

gnomad_qc.v5.resources.annotations.group_membership(test=False, data_set='aou', environment='rwb')[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”.
environment (str) – Environment to use. Default is “rwb”. Must be one of “rwb” or “batch”.

Return type:

VersionedTableResource

Returns:

Hail Table containing group membership annotations.

gnomad_qc.v5.resources.annotations.qual_hists(test=False, environment='rwb')[source]

Get the quality histograms annotation table.

Parameters:

test (bool) – Whether to use a tmp path for tests. Default is False.
environment (str) – Environment to use for quality histograms. Must be one of “rwb” or “batch”.

Return type:

VersionedTableResource

Returns:

Hail Table containing quality histogram annotations.

gnomad_qc.v5.resources.annotations.coverage_and_an_path(test=False, data_set='aou', environment='rwb')[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”.
environment (str) – Environment to use. Default is “rwb”. Must be one of “rwb”, “batch”, or “dataproc”.

Return type:

VersionedTableResource

Returns:

Coverage and allele number Hail Table.

gnomad_qc.v5.resources.annotations.get_freq(version='5.0', data_type='genomes', test=False, data_set='aou', environment='rwb')[source]

Get the frequency annotation Table for v5.

Parameters:

version (str) – Version of annotation path to return.
data_type (str) – Data type of annotation resource (“genomes” or “exomes”).
test (bool) – Whether to use a tmp path for testing.
data_set (str) – Data set of annotation resource. Default is “aou”.
environment (str) – Environment to use. Default is “rwb”. Must be one of “rwb”, “batch”, or “dataproc”.

Return type:

TableResource

Returns:

Hail Table containing frequency annotations.

gnomad_qc.v5.resources.annotations.get_info_ht(test=False, environment='batch')[source]

Get the gnomAD v5 (AoU genomes only) info VersionedTableResource.

Parameters:

test (bool) – Whether to use a tmp path for testing.
environment (str) – Environment to use. Default is “batch”. Must be one of “rwb” or “batch”.

Return type:

VersionedTableResource

Returns:

Info VersionedTableResource.

gnomad_qc.v5.resources.annotations.info_vcf_path(version='5.0', test=False, environment='batch')[source]

Path to sites VCF (input information for running VQSR).

Parameters:

version (str) – Version of annotation path to return.
test (bool) – Whether to use a tmp path for testing.
environment (str) – Environment to use. Must be one of “rwb” or “batch”. Default is “batch”.

Return type:

str

Returns:

String for the path to the info VCF.

gnomad_qc.v5.resources.annotations.get_aou_vcf_header(environment='batch')[source]

Get path to AoU annotation sites-only VCF header.

This is needed for proper import of the sites-only VCF as the QUALapprox annotation is stated in the previous header as an int but is actually a float.

Parameters:: environment (str) – Environment to use. Default is “batch”. Must be one of “rwb” or “batch”.
Return type:: str
Returns:: Path to the VCF header file.

gnomad_qc.v5.resources.annotations.get_aou_annotated_sites_only_vcf(environment='batch')[source]

Get path to AoU sites-only VCF with annotations needed for variant QC.

Parameters:: environment (str) – Environment to use. Default is “batch”. Must be one of “rwb” or “batch”.
Return type:: str
Returns:: Path to the annotated sites-only VCF.

gnomad_qc.v5.resources.annotations.get_vep(test=False, vep_version='105', environment='batch')[source]

Get the gnomAD v5 VEP annotation VersionedTableResource.

Parameters:

test (bool) – Whether to use a tmp path for analysis of the test Table instead of the full v5 Table.
vep_version (str) – VEP version to use (e.g., “105”, “115”). Default is “105”.
environment (str) – Environment to use. Default is “batch”. Must be one of “rwb”, “batch”, or “dataproc”.

Return type:

VersionedTableResource

Returns:

gnomAD v5 VEP VersionedTableResource.

gnomad_qc.v5.resources.annotations.validate_vep_path(test=False, vep_version='105', environment='batch')[source]

Get the gnomAD v5 VEP annotation VersionedTableResource for validation counts.

Parameters:

test (bool) – Whether to use a tmp path for analysis of the test VDS instead of the full v5 VDS.
vep_version (str) – VEP version to use (e.g., “105”, “115”). Default is “105”.
environment (str) – Environment to use. Default is “batch”. Must be one of “rwb”, “batch”, or “dataproc”.

Return type:

VersionedTableResource

Returns:

gnomAD v5 VEP VersionedTableResource containing validity check.