gnomad_qc.v4.resources.assessment
Script containing assessment related resources.
Module Functions
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Get the filtering groups used in the summary stats. |
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Get per-sample variant counts and other information as generated by Hail's Sample QC module. |
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.