Variant Annotation and Identifier Conversion: 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 variant consequences and annotations¶

dnakit.databases.ensembl_var_get_variant_consequences(*, variant_id, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`variant_id`	string	Required	dbSNP rsID of the variant. Examples: 'rs429358' (APOE), 'rs7903146' (TCF7L2), 'rs1042779'.
`species`	string	None	Species name. Default 'human'. Examples: 'human', 'homo_sapiens'.
`verbose`	bool	True	Progress flag.

Annotate HGVS variants with Ensembl VEP¶

dnakit.databases.ensembl_vep_annotate_hgvs(*, hgvs_notation, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`hgvs_notation`	string	Required	Variant in HGVS notation. Supports protein (p.), coding DNA (c.), and genomic (g.) notation. Examples: 'BRAF:p.Val600Glu', 'ENST00000366667:c.803C>T', 'NC_000007.14:g.140753336A>T'.
`species`	string	None	Species name. Default: 'human'. Other options: 'mouse', 'rat', 'zebrafish', etc.
`verbose`	bool	True	Progress flag.

Annotate rsID variants with Ensembl VEP¶

dnakit.databases.ensembl_vep_annotate_rsid(*, variant_id=None, rsid=None, rs_id=None, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`variant_id`	string	None	dbSNP rs identifier. Examples: 'rs7903146' (TCF7L2, type 2 diabetes), 'rs429358' (APOE, Alzheimer's), 'rs1801133' (MTHFR C677T). Aliases: rsid, rs_id.
`rsid`	string	None	Alias for variant_id. dbSNP rs identifier (e.g., 'rs7903146').
`rs_id`	string	None	Alias for variant_id. dbSNP rs identifier (e.g., 'rs7903146').
`species`	string	None	Species name. Default: 'human'.
`verbose`	bool	True	Progress flag.

Annotate genomic variants with Ensembl VEP¶

dnakit.databases.ensembl_vep_region(*, species, region, allele=None, AncestralAllele=None, Blosum62=None, CADD=None, Conservation=None, DisGeNET=None, GeneSplicer=None, GO=None, LoF=None, MaxEntScan=None, Phenotypes=None, SIFT=None, PolyPhen=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`species`	string	Required	Species (e.g., 'human', 'homo_sapiens')
`region`	string	Required	Genomic region with variant (e.g., '21:25891796-25891796')
`allele`	string	None	Allele argument for a region variant in Ensembl VEP format.
`AncestralAllele`	integer	None	Include ancestral allele information
`Blosum62`	integer	None	Include BLOSUM62 protein conservation score
`CADD`	integer	None	Include CADD scores
`Conservation`	integer	None	Include conservation scores
`DisGeNET`	integer	None	Include DisGeNET disease associations
`GeneSplicer`	integer	None	Include GeneSplicer predictions
`GO`	integer	None	Include Gene Ontology terms
`LoF`	integer	None	Include Loss-of-Function predictions
`MaxEntScan`	integer	None	Include MaxEntScan splice predictions
`Phenotypes`	integer	None	Include phenotype annotations
`SIFT`	string	None	SIFT prediction: p=prediction, s=score, b=both
`PolyPhen`	string	None	PolyPhen prediction: p=prediction, s=score, b=both
`verbose`	bool	True	Progress flag.

Convert variant identifiers and HGVS representations¶

dnakit.databases.ensembl_vep_variant_recoder(*, variant_id, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`variant_id`	string	Required	Variant identifier to recode. Accepts: rsID (e.g., 'rs429358'), HGVS notation (e.g., 'AGT:c.803T>C'), SPDI (e.g., 'NC_000019.10:44908683:T:C').
`species`	string	None	Species name. Default: 'human'.
`verbose`	bool	True	Progress flag.

Annotate GRCh38 variants with FAVOR¶

dnakit.databases.favor_annotate_variant(*, variant, verbose=True)

Parameter	Type	Required / default	Description and constraints
`variant`	string	Required	GRCh38 SNV/indel as chr-pos-ref-alt. Accepts '19-44908822-C-T', 'chr19:44908822:C:T', etc.
`verbose`	bool	True	Progress flag.

Retrieve variant annotations by HGVS or rsID¶

dnakit.databases.my_variant_get_variant_annotation(*, variant_id, fields=None, assembly=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`variant_id`	string	Required	HGVS variant ID (e.g., 'chr1:g.2186318G>A') or rsID (e.g., 'rs123'). An HGVS id must be expressed in the assembly given by the 'assembly' parameter.
`fields`	string	None	Fields to return. Useful fields: dbsnp, clinvar, cadd, gnomad_genome, gnomad_exome, dbnsfp (functional predictions).
`assembly`	string	None	Reference genome assembly for both the HGVS variant_id and the returned coordinates: 'hg19' (GRCh37, the default) or 'hg38' (GRCh38).
`verbose`	bool	True	Progress flag.

Search variants by gene, position or clinical significance¶

dnakit.databases.my_variant_query_variants(*, query=None, fields=None, size=None, assembly=None, variant_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`query`	string	None	Search query. Examples: 'rs58991260' (rsID), 'chr7:g.55249071G>A' (HGVS), 'clinvar.gene.symbol:BRCA1' (gene in ClinVar), 'cadd.phred:>30' (high CADD score).
`fields`	string	None	Comma-separated fields to return. Common: dbsnp, clinvar, cadd, gnomad_genome, dbnsfp.
`size`	integer	None	Maximum number of results (1-100).
`assembly`	string	None	Reference genome assembly for the coordinates in the query and in the results: 'hg19' (GRCh37, the default) or 'hg38' (GRCh38).
`variant_id`	string	None	DNAKit optional alias for query
`verbose`	bool	True	Progress flag.

Validate and convert HGVS variant descriptions¶

dnakit.databases.variant_validator_validate_variant(*, genome_build, variant_description, select_transcripts, verbose=True)

Parameter	Type	Required / default	Description and constraints
`genome_build`	string	Required	Reference genome assembly: 'GRCh37' (hg19) or 'GRCh38' (hg38)
`variant_description`	string	Required	HGVS variant description (e.g., 'NM_007294.4:c.5266dup' for BRCA1 c.5266dupC, 'NM_000179.3:c.943C>T', 'chr17:g.43092919del')
`select_transcripts`	string	Required	Transcript to validate against (e.g., 'NM_007294.4'). Use 'all' to get all transcripts for a genomic variant.
`verbose`	bool	True	Progress flag.