Gwas Sumstats Tools

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

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

Available Tools

GWASSumStats_get_region_associations (Type: GWASSumStatsTool)

Query full GWAS summary statistics for variants in a chromosomal region. Returns variant-level as…

GWASSumStats_get_region_associations tool specification

Tool Information:

  • Name: GWASSumStats_get_region_associations

  • Type: GWASSumStatsTool

  • Description: Query full GWAS summary statistics for variants in a chromosomal region. Returns variant-level association data including p-values, effect sizes (beta/OR), allele frequencies, and study/trait information. Unlike gwas_search_associations (which returns curated top hits), this endpoint provides complete summary statistics from deposited studies. Filter by chromosome region, p-value threshold, and optionally by specific study.

Parameters:

  • chromosome (integer) (required) Chromosome number (1-22, or 23 for X).

  • bp_lower (integer) (required) Start position of the region (GRCh38 coordinates).

  • bp_upper (integer) (required) End position of the region (GRCh38 coordinates).

  • p_upper ([‘number’, ‘null’]) (optional) Maximum p-value threshold (default 5e-8 for genome-wide significance). Use larger values like 0.001 to include suggestive hits.

  • study_accession ([‘string’, ‘null’]) (optional) Filter by specific GWAS study accession (e.g., ‘GCST002245’). Get study IDs from GWASSumStats_list_studies or GWASSumStats_get_trait_studies.

  • size ([‘integer’, ‘null’]) (optional) Maximum number of variants to return (default 50, max 1000).

Example Usage:

query = {
    "name": "GWASSumStats_get_region_associations",
    "arguments": {
        "chromosome": 10,
        "bp_lower": 10,
        "bp_upper": 10
    }
}
result = tu.run(query)

GWASSumStats_get_trait_studies (Type: GWASSumStatsTool)

Get GWAS studies with deposited summary statistics for a specific EFO trait. Returns study access…

GWASSumStats_get_trait_studies tool specification

Tool Information:

  • Name: GWASSumStats_get_trait_studies

  • Type: GWASSumStatsTool

  • Description: Get GWAS studies with deposited summary statistics for a specific EFO trait. Returns study accession IDs for studies that have full variant-level summary statistics. Use EFO trait IDs like ‘EFO_0000249’ (Alzheimer disease), ‘EFO_0001645’ (coronary heart disease), ‘EFO_0000253’ (asthma), ‘EFO_0001359’ (type 2 diabetes). Get EFO IDs from ols_search_efo_terms or gwas_search_studies.

Parameters:

  • trait_id (string) (required) EFO trait ontology ID (e.g., ‘EFO_0000249’ for Alzheimer disease, ‘EFO_0001645’ for coronary heart disease, ‘EFO_0001359’ for type 2 diabetes).

Example Usage:

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

GWASSumStats_list_studies (Type: GWASSumStatsTool)

List GWAS studies that have deposited full summary statistics with the EBI GWAS Catalog. Unlike t…

GWASSumStats_list_studies tool specification

Tool Information:

  • Name: GWASSumStats_list_studies

  • Type: GWASSumStatsTool

  • Description: List GWAS studies that have deposited full summary statistics with the EBI GWAS Catalog. Unlike the main GWAS Catalog (which stores curated top hits), studies listed here have complete variant-level summary statistics available for download and query. Returns study accession IDs that can be used as filters in GWASSumStats_get_region_associations.

Parameters:

  • size ([‘integer’, ‘null’]) (optional) Number of studies to return (default 20, max 100).

Example Usage:

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