Eva Tools#

Configuration File: eva_tools.json Tool Type: Local Tools Count: 4

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

Available Tools#

EVA_get_clustered_variant_by_rs (Type: BaseRESTTool)#

Resolve an EVA clustered-variant RS accession to its canonical assembly/contig/position record us…

EVA_get_clustered_variant_by_rs tool specification

Tool Information:

  • Name: EVA_get_clustered_variant_by_rs

  • Type: BaseRESTTool

  • Description: Resolve an EVA clustered-variant RS accession to its canonical assembly/contig/position record using the EVA accessioning (identifiers) service. This is distinct from EVA’s variant-DATA API (webservices/rest) used by the other EVA tools: the accessioning API (webservices/identifiers) maps an RS accession to its definitive coordinate record (assemblyAccession, taxonomyAccession, contig, start, variant type). The RS accession is the numeric clustered-variant id (e.g. 429358), not the ‘rs’ prefixed dbSNP string. Returns a list of accession records (usually one).

Parameters:

  • accession (string) (required) EVA clustered-variant RS accession (numeric, no ‘rs’ prefix). Examples: ‘429358’ (human APOE region, GRCh38 contig CM000681.2 start 44908684), ‘3091781465’ (horse clustered variant)

Example Usage:

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

EVA_get_variants_by_gene (Type: BaseRESTTool)#

Get genetic variants from the European Variation Archive (EVA) for a specific gene. Results use e…

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. Results use exact skip pagination: start with offset=0 and continue with metadata.next_offset while metadata.has_more is true, always keeping the same limit because EVA aligns skip to page boundaries. metadata.total_results is exact. Returns allele frequencies, study sources, and variant type. 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) Variants per page (default 20, maximum 1000)

  • offset (integer) (optional) Zero-based variant offset. It must be a multiple of limit; continue with metadata.next_offset using the same limit.

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 EVA within a genomic region. Start with offset=0 and continue with meta…

EVA_get_variants_by_region tool specification

Tool Information:

  • Name: EVA_get_variants_by_region

  • Type: BaseRESTTool

  • Description: Get genetic variants from EVA within a genomic region. Start with offset=0 and continue with metadata.next_offset while metadata.has_more is true, always keeping the same limit because EVA aligns skip to page boundaries. EVA can report numTotalResults=0 on non-empty region pages; ToolUniverse detects this conflict, exposes upstream_total_inconsistent, and uses full-page continuation until a short page establishes the exact total. Returns SNVs, indels, and structural variants.

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) Variants per page (default 20, maximum 1000)

  • offset (integer) (optional) Zero-based variant offset. It must be a multiple of limit; continue with metadata.next_offset using the same limit.

Example Usage:

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

EVA_list_studies (Type: BaseRESTTool)#

List EVA variant studies with deterministic local limit/offset pagination. The upstream endpoint …

EVA_list_studies tool specification

Tool Information:

  • Name: EVA_list_studies

  • Type: BaseRESTTool

  • Description: List EVA variant studies with deterministic local limit/offset pagination. The upstream endpoint returns the complete study list, ignores pagination parameters, and can vary raw order between identical calls. ToolUniverse sorts by studyId before paging. Continue with metadata.next_offset while metadata.has_more is true.

Parameters:

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

  • limit (integer) (optional) Studies per deterministic local page (default 20, max 1000).

  • offset (integer) (optional) Zero-based offset after sorting by studyId. Continue with metadata.next_offset.

Example Usage:

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