gnomad_qc.v4.resources.assessment

Script containing assessment related resources.

Module Functions

gnomad_qc.v4.resources.assessment.get_summary_stats_filtering_groups([...])

Get the filtering groups used in the summary stats.

gnomad_qc.v4.resources.assessment.get_per_sample_counts([...])

Get per-sample variant counts and other information as generated by Hail's Sample QC module.

gnomad_qc.v4.resources.assessment.release_summary_stats([...])

Retrieve versioned resource for release summary stats Table.

gnomad_qc.v4.resources.assessment.release_lof([...])

Retrieve versioned resource for release LOF stats MatrixTable or Table.

Script containing assessment related resources.

gnomad_qc.v4.resources.assessment.get_summary_stats_filtering_groups(data_type='exomes', test=False, suffix=None)[source]

Get the filtering groups used in the summary stats.

Parameters:

  • data_type (str) – Data type for summary stats filtering groups, e.g. “exomes” or “genomes”.

  • test (bool) – Whether to use a tmp path for analysis of the test VDS instead of the full v4 VDS.

  • suffix (str) – Additional name to append, containing some method or filtering information.

Return type:

VersionedTableResource

Returns:

Filtering groups used in the summary stats.

gnomad_qc.v4.resources.assessment.get_per_sample_counts(test=False, data_type='exomes', suffix=None, autosomes=False, sex_chr=False, aggregated=False, by_ancestry=False, by_subset=False)[source]

Get per-sample variant counts and other information as generated by Hail’s Sample QC module.

Parameters:

  • test (bool) – Whether to use a tmp path for analysis of the test VDS instead of the full v4 VDS.

  • data_type (str) – Data type used in sample QC, e.g. “exomes” or “genomes”.

  • suffix (str) – Additional name to append, containing some method or filtering information.

  • autosomes (bool) – Whether to use the autosomes only per-sample counts table. Default is False.

  • sex_chr (bool) – Whether to use the sex chromosomes only per-sample counts table. Default is False.

  • aggregated (bool) – Whether to use the aggregated per-sample counts table. Default is False.

  • by_ancestry (bool) – Whether to use the per-sample counts table stratified by ancestry. Default is False.

  • by_subset (bool) – Whether to use the per-sample counts table stratified by subset. Default is False.

Return type:

VersionedTableResource

Returns:

Per sample variant counts table.

gnomad_qc.v4.resources.assessment.release_summary_stats(test=False, data_type='exomes', filter_name=None)[source]

Retrieve versioned resource for release summary stats Table.

Parameters:

  • test (bool) – Whether to use a tmp path for testing. Default is False.

  • data_type (str) – ‘exomes’ or ‘genomes’. Default is ‘exomes’.

  • filter_name (Optional[str]) –

Return type:

VersionedTableResource

Returns:

Summary stats Table.

gnomad_qc.v4.resources.assessment.release_lof(test=False, data_type='exomes', mt=False)[source]

Retrieve versioned resource for release LOF stats MatrixTable or Table.

Parameters:

  • test (bool) – Whether to use a tmp path for testing. Default is False.

  • data_type (str) – ‘exomes’ or ‘genomes’. Default is ‘exomes’.

  • mt (bool) – Whether to return the lof MatrixTable instead of Table. Default is False.

Return type:

VersionedTableResource

Returns:

release LOF stats MatrixTable or Table.