Eva Tools

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

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

Available Tools

EVA_get_variants_by_gene (Type: BaseRESTTool)

Get genetic variants from the European Variation Archive (EVA) for a specific gene. EVA is hosted…

EVA_get_variants_by_gene tool specification

Tool Information:

  • Name: EVA_get_variants_by_gene

  • Type: BaseRESTTool

  • Description: Get genetic variants from the European Variation Archive (EVA) for a specific gene. EVA is hosted at EBI and aggregates variant data from multiple studies including ClinVar, dbSNP, and population sequencing projects. Returns variants with allele frequencies, study sources, and variant type. The gene name uses HGNC symbols (e.g., ‘BRCA1’, ‘TP53’, ‘EGFR’). Species defaults to human GRCh38.

Parameters:

  • gene (string) (required) Gene symbol (HGNC format, e.g., ‘BRCA1’, ‘TP53’, ‘EGFR’, ‘BRCA2’, ‘APOE’)

  • species (string) (optional) Species and assembly (e.g., ‘hsapiens_grch38’, ‘hsapiens_grch37’, ‘mmusculus_grcm38’)

  • limit (integer) (optional) Maximum number of variants to return (default 20, max ~1000)

Example Usage:

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

EVA_get_variants_by_region (Type: BaseRESTTool)

Get genetic variants from the European Variation Archive (EVA) within a specific genomic region. …

EVA_get_variants_by_region tool specification

Tool Information:

  • Name: EVA_get_variants_by_region

  • Type: BaseRESTTool

  • Description: Get genetic variants from the European Variation Archive (EVA) within a specific genomic region. Returns all known variants in the specified chromosomal coordinate range, including SNVs, indels, and structural variants with allele frequencies from multiple studies. Useful for scanning variant hotspots or checking variants in regulatory regions. The endpoint URL uses ‘chromosome:start-end’ format.

Parameters:

  • region (string) (required) Genomic region in ‘chr:start-end’ format (e.g., ‘17:41200000-41210000’, ‘7:140753300-140753400’, ‘19:44905700-44910000’)

  • species (string) (optional) Species and assembly (e.g., ‘hsapiens_grch38’, ‘hsapiens_grch37’)

  • limit (integer) (optional) Maximum number of variants to return

Example Usage:

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

EVA_list_studies (Type: BaseRESTTool)

List all variant studies available in the European Variation Archive (EVA) for a given species. R…

EVA_list_studies tool specification

Tool Information:

  • Name: EVA_list_studies

  • Type: BaseRESTTool

  • Description: List all variant studies available in the European Variation Archive (EVA) for a given species. Returns study accessions (e.g., PRJEB84021) that have submitted variant data. Useful for discovering available datasets before querying variants. Each study typically corresponds to a population sequencing project or variant calling pipeline.

Parameters:

  • species (string) (optional) Species and assembly (e.g., ‘hsapiens_grch38’, ‘hsapiens_grch37’, ‘mmusculus_grcm38’)

Example Usage:

query = {
    "name": "EVA_list_studies",
    "arguments": {
    }
}
result = tu.run(query)