gnomad_qc.v4.resources.basics

Script containing generic resources.

Module Functions

`gnomad_qc.v4.resources.basics.get_gnomad_v4_vds`([...])	Get gnomAD v4 data with desired filtering and metadata annotations.
`gnomad_qc.v4.resources.basics.get_gnomad_v4_genomes_vds`([...])	Get gnomAD v4 genomes VariantDataset with desired filtering and metadata annotations.
`gnomad_qc.v4.resources.basics.qc_temp_prefix`([...])	Return path to temporary QC bucket.
`gnomad_qc.v4.resources.basics.get_checkpoint_path`(name)	Create a checkpoint path for Table or MatrixTable.
`gnomad_qc.v4.resources.basics.get_logging_path`(name)	Create a path for Hail log files.
`gnomad_qc.v4.resources.basics.add_meta`(mt[, ...])	Add metadata to MT in 'meta_name' column.
`gnomad_qc.v4.resources.basics.calling_intervals`(...)	Return path to capture intervals Table.

Script containing generic resources.

gnomad_qc.v4.resources.basics.get_gnomad_v4_vds(split=False, remove_hard_filtered_samples=True, remove_hard_filtered_samples_no_sex=False, high_quality_only=False, keep_controls=False, release_only=False, controls_only=False, test=False, n_partitions=None, filter_partitions=None, chrom=None, autosomes_only=False, sex_chr_only=False, filter_variant_ht=None, filter_intervals=None, split_reference_blocks=True, remove_dead_alleles=True, annotate_meta=False, entries_to_keep=None, annotate_het_non_ref=False)[source]

Get gnomAD v4 data with desired filtering and metadata annotations.

Parameters:

split (bool) – Perform split on VDS - Note: this will perform a split on the VDS rather than grab an already split VDS.
remove_hard_filtered_samples (bool) – Whether to remove samples that failed hard filters (only relevant after hard filtering is complete).
remove_hard_filtered_samples_no_sex (bool) – Whether to remove samples that failed non sex inference hard filters (only relevant after pre-sex imputation hard filtering is complete).
high_quality_only (bool) – Whether to filter the VDS to only high quality samples (only relevant after outlier filtering is complete).
keep_controls (bool) – Whether to keep control samples when filtering the VDS to a subset of samples.
release_only (bool) – Whether to filter the VDS to only samples available for release (can only be used if metadata is present).
controls_only (bool) – Whether to filter the VDS to only control samples.
test (bool) – Whether to use the test VDS instead of the full v4 VDS.
n_partitions (Optional[int]) – Optional argument to read the VDS with a specific number of partitions.
filter_partitions (Optional[List[int]]) – Optional argument to filter the VDS to specific partitions.
chrom (Union[str, List[str], Set[str], None]) – Optional argument to filter the VDS to a specific chromosome(s).
autosomes_only (bool) – Whether to filter the VDS to autosomes only. Default is False.
sex_chr_only (bool) – Whether to filter the VDS to sex chromosomes only. Default is False.
filter_variant_ht (Optional[Table]) – Optional argument to filter the VDS to a specific set of variants. Only supported when splitting the VDS.
filter_intervals (Optional[List[Union[str, tinterval]]]) – Optional argument to filter the VDS to specific intervals.
split_reference_blocks (bool) – Whether to split the reference data at the edges of the intervals defined by filter_intervals. Default is True.
remove_dead_alleles (bool) – Whether to remove dead alleles from the VDS when removing withdrawn UKB samples. Default is True.
annotate_meta (bool) – Whether to annotate the VDS with the sample QC metadata. Default is False.
entries_to_keep (Optional[List[str]]) – Optional argument to keep only specific entries in the returned VDS. If splitting the VDS, use the global entries (e.g. ‘GT’) instead of the local entries (e.g. ‘LGT’) to keep.
annotate_het_non_ref (bool) – Whether to annotate non reference heterozygotes (as ‘_het_non_ref’) to the variant data. Default is False.

Return type:

VariantDataset

Returns:

gnomAD v4 dataset with chosen annotations and filters.

gnomad_qc.v4.resources.basics.get_gnomad_v4_genomes_vds(split=False, remove_hard_filtered_samples=True, release_only=False, annotate_meta=False, test=False, filter_partitions=None, chrom=None, autosomes_only=False, sex_chr_only=False, filter_variant_ht=None, filter_intervals=None, split_reference_blocks=True, entries_to_keep=None, annotate_het_non_ref=False)[source]

Get gnomAD v4 genomes VariantDataset with desired filtering and metadata annotations.

Parameters:

split (bool) – Perform split on VDS - Note: this will perform a split on the VDS rather than grab an already split VDS.
remove_hard_filtered_samples (bool) – Whether to remove samples that failed hard filters (only relevant after sample QC).
release_only (bool) – Whether to filter the VDS to only samples available for release (can only be used if metadata is present).
annotate_meta (bool) – Whether to add v4 genomes metadata to VDS variant_data in ‘meta’ column.
test (bool) – Whether to use the test VDS instead of the full v4 genomes VDS.
filter_partitions (Optional[List[int]]) – Optional argument to filter the VDS to specific partitions in the provided list.
chrom (Union[str, List[str], Set[str], None]) – Optional argument to filter the VDS to a specific chromosome(s).
autosomes_only (bool) – Whether to filter the VDS to autosomes only. Default is False.
sex_chr_only (bool) – Whether to filter the VDS to sex chromosomes only. Default is False.
filter_variant_ht (Optional[Table]) – Optional argument to filter the VDS to a specific set of variants. Only supported when splitting the VDS.
filter_intervals (Optional[List[Union[str, tinterval]]]) – Optional argument to filter the VDS to specific intervals.
split_reference_blocks (bool) – Whether to split the reference data at the edges of the intervals defined by filter_intervals. Default is True.
entries_to_keep (Optional[List[str]]) – Optional argument to keep only specific entries in the returned VDS. If splitting the VDS, use the global entries (e.g. ‘GT’) instead of the local entries (e.g. ‘LGT’) to keep.
annotate_het_non_ref (bool) – Whether to annotate non reference heterozygotes (as ‘_het_non_ref’) to the variant data. Default is False.

Return type:

VariantDataset

Returns:

gnomAD v4 genomes VariantDataset with chosen annotations and filters.

gnomad_qc.v4.resources.basics.qc_temp_prefix(version='4.1', data_type='exomes')[source]

Return path to temporary QC bucket.

Parameters:

version (str) – Version of annotation path to return.
data_type – One of ‘exomes’ or ‘genomes’. Default is ‘exomes’.

Return type:

str

Returns:

Path to bucket with temporary QC data

gnomad_qc.v4.resources.basics.get_checkpoint_path(name, version='4.1', mt=False)[source]

Create a checkpoint path for Table or MatrixTable.

Parameters:

name (str) – Name of intermediate Table/MatrixTable
version (str) – Version of annotation path to return
mt (bool) – Whether path is for a MatrixTable, default is False
name –
mt –

Return type:

str

Returns:

Output checkpoint path

gnomad_qc.v4.resources.basics.get_logging_path(name, version='4.1')[source]

Create a path for Hail log files.

Parameters:

name (str) – Name of log file
version (str) – Version of annotation path to return

Return type:

str

Returns:

Output log path

gnomad_qc.v4.resources.basics.add_meta(mt, version='4.0', meta_name='meta')[source]

Add metadata to MT in ‘meta_name’ column.

Parameters:

mt (MatrixTable) – MatrixTable to which ‘meta_name’ annotation should be added
version (str) –
meta_name (str) –

Return type:

MatrixTable

Returns:

MatrixTable with metadata added in a ‘meta’ column

gnomad_qc.v4.resources.basics.calling_intervals(interval_name, calling_interval_padding)[source]

Return path to capture intervals Table.

Parameters:

interval_name (str) – One of ‘ukb’, ‘broad’, ‘intersection’ or ‘union’.
calling_interval_padding (int) – Padding around calling intervals. Available options are 0 or 50.

Return type:

TableResource

Returns:

Calling intervals resource.