Structural Variant Queries: parameters and notes¶

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

Retrieve Ensembl structural variants in an interval¶

dnakit.databases.ensembl_get_structural_variants(*, species, region=None, feature=None, chrom=None, start=None, end=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`species`	string	Required	Species name (e.g., 'human', 'homo_sapiens').
`region`	string	None	Genomic region in format 'chr:start-end' (e.g., '17:43044295-43125370'). Maximum 5Mb.
`feature`	string	None	Feature type to retrieve. Fixed to 'structural_variation' for this tool.
`chrom`	string	None	Chromosome identifier; provide with start and end.
`start`	integer	None	Region start; this parameter branch uses Ensembl 1-based inclusive coordinates.
`end`	integer	None	Region end; this parameter branch uses Ensembl 1-based inclusive coordinates.
`verbose`	bool	True	Progress flag.

Retrieve Ensembl structural variant details¶

dnakit.databases.ensembl_get_sv_detail(*, species, id=None, sv_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`species`	string	Required	Species name (e.g., 'human', 'homo_sapiens').
`id`	string	None	Structural variant accession from Ensembl/DGVa (e.g., 'nsv2769779', 'esv3647486'). Use ensembl_get_structural_variants to find IDs.
`sv_id`	string	None	DNAKit optional alias for id
`verbose`	bool	True	Progress flag.

Find gnomAD structural variants by gene¶

dnakit.databases.gnomad_get_sv_by_gene(*, gene_symbol, reference_genome=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene_symbol`	string	Required	Gene symbol (e.g., 'BRCA1', 'TP53', 'MECP2')
`reference_genome`	string	None	Reference genome assembly.
`verbose`	bool	True	Progress flag.

Find gnomAD structural variants by genomic interval¶

dnakit.databases.gnomad_get_sv_by_region(*, chrom, start, stop=None, reference_genome=None, end=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`chrom`	string	Required	Chromosome (e.g., '17', 'X').
`start`	integer	Required	Start position (1-based, GRCh38 by default).
`stop`	integer	None	Stop position.
`reference_genome`	string	None	Reference genome assembly.
`end`	integer	None	DNAKit optional alias for stop
`verbose`	bool	True	Progress flag.

Retrieve gnomAD structural variant details¶

dnakit.databases.gnomad_get_sv_detail(*, variant_id=None, dataset=None, sv_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`variant_id`	string	None	gnomAD structural variant ID. GRCh38/v4 IDs look like 'DEL_chr17_24e4872b'; GRCh37/v2.1 IDs look like 'DEL_1_1937'.
`dataset`	string	None	Optional SV callset override. Defaults to the callset auto-detected from the variant ID format (gnomad_sv_r2_1 for GRCh37-style IDs, gnomad_sv_r4 otherwise). Set explicitly only to query a v2.1 subset such as gnomad_sv_r2_1_controls.
`sv_id`	string	None	DNAKit optional alias for variant_id
`verbose`	bool	True	Progress flag.