Ensembl Vep Tools

Configuration File: ensembl_vep_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the ensembl_vep_tools.json configuration file.

Available Tools

EnsemblVEP_annotate_hgvs (Type: EnsemblVEPTool)

Predict functional consequences of a genetic variant using HGVS notation via the Ensembl Variant …

EnsemblVEP_annotate_hgvs tool specification

Tool Information:

  • Name: EnsemblVEP_annotate_hgvs

  • Type: EnsemblVEPTool

  • Description: Predict functional consequences of a genetic variant using HGVS notation via the Ensembl Variant Effect Predictor (VEP). Returns impact on genes, transcripts, and proteins including SIFT/PolyPhen pathogenicity scores, consequence types, amino acid changes, and colocated known variants. HGVS notation examples: ‘BRAF:p.Val600Glu’ (protein), ‘ENST00000366667:c.803C>T’ (coding DNA). This complements the existing region-based VEP tool by accepting standard clinical variant nomenclature.

Parameters:

  • 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) (optional) Species name. Default: ‘human’. Other options: ‘mouse’, ‘rat’, ‘zebrafish’, etc.

Example Usage:

query = {
    "name": "EnsemblVEP_annotate_hgvs",
    "arguments": {
        "hgvs_notation": "example_value"
    }
}
result = tu.run(query)

EnsemblVEP_annotate_rsid (Type: EnsemblVEPTool)

Predict functional consequences of a genetic variant using its dbSNP rs identifier via the Ensemb…

EnsemblVEP_annotate_rsid tool specification

Tool Information:

  • Name: EnsemblVEP_annotate_rsid

  • Type: EnsemblVEPTool

  • Description: Predict functional consequences of a genetic variant using its dbSNP rs identifier via the Ensembl Variant Effect Predictor (VEP). Returns impact on genes, transcripts, and proteins including SIFT/PolyPhen scores, consequence types, amino acid changes, and colocated variants. Useful when you have a variant’s rs number from GWAS, clinical reports, or literature. Example: ‘rs7903146’ (TCF7L2 T2D variant), ‘rs429358’ (APOE Alzheimer variant).

Parameters:

  • variant_id (string) (required) dbSNP rs identifier. Examples: ‘rs7903146’ (TCF7L2, type 2 diabetes), ‘rs429358’ (APOE, Alzheimer’s), ‘rs1801133’ (MTHFR C677T).

  • species (string) (optional) Species name. Default: ‘human’.

Example Usage:

query = {
    "name": "EnsemblVEP_annotate_rsid",
    "arguments": {
        "variant_id": "example_value"
    }
}
result = tu.run(query)

EnsemblVEP_variant_recoder (Type: EnsemblVEPTool)

Convert genetic variant identifiers between different nomenclature formats using the Ensembl Vari…

EnsemblVEP_variant_recoder tool specification

Tool Information:

  • Name: EnsemblVEP_variant_recoder

  • Type: EnsemblVEPTool

  • Description: Convert genetic variant identifiers between different nomenclature formats using the Ensembl Variant Recoder. Given a variant ID (e.g., rs number), returns equivalent representations in HGVS genomic (hgvsg), HGVS coding (hgvsc), HGVS protein (hgvsp), and SPDI format. Essential for cross-referencing variants across databases that use different notation systems. Example: ‘rs429358’ returns HGVS coding notation for all APOE transcripts.

Parameters:

  • 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) (optional) Species name. Default: ‘human’.

Example Usage:

query = {
    "name": "EnsemblVEP_variant_recoder",
    "arguments": {
        "variant_id": "example_value"
    }
}
result = tu.run(query)