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)#

RETIRED: region-level summary statistics are no longer served over REST. EBI retired /gwas/summar…

GWASSumStats_get_region_associations tool specification

Tool Information:

  • Name: GWASSumStats_get_region_associations

  • Type: GWASSumStatsTool

  • Description: RETIRED: region-level summary statistics are no longer served over REST. EBI retired /gwas/summary-statistics/api (410 on every path) and the v2 API serves associations only per study, ignoring chromosome, position and p-value filters. This tool now returns an error naming the FTP location (ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/) where the per-study files live, to be queried with tabix. Use GWASSumStats_get_trait_studies to find the accessions to download.

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)#

Find GWAS Catalog studies for a trait, matched on the EFO trait LABEL rather than an ontology id….

GWASSumStats_get_trait_studies tool specification

Tool Information:

  • Name: GWASSumStats_get_trait_studies

  • Type: GWASSumStatsTool

  • Description: Find GWAS Catalog studies for a trait, matched on the EFO trait LABEL rather than an ontology id. The match is a case-insensitive substring of the label, so ‘alzheimer’ returns more studies than ‘Alzheimer disease’ and both are valid: use a shorter term to cast wider, a fuller label to narrow. Passing trait_id returns an error explaining this rather than an empty result.

Parameters:

  • trait (string) (optional) Text matched case-insensitively against the EFO trait label, e.g. ‘alzheimer’ (438 studies), ‘Alzheimer disease’ (250), ‘body mass index’, ‘diabetes’.

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

  • trait_id ([‘string’, ‘null’]) (optional) Deprecated. An ontology id such as ‘EFO_0000249’; the API filters on the label, so this returns an error telling you how to resolve it.

Example Usage:

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

GWASSumStats_list_studies (Type: GWASSumStatsTool)#

List studies in the EBI GWAS Catalog, newest API (v2). Returns the study accession with its repor…

GWASSumStats_list_studies tool specification

Tool Information:

  • Name: GWASSumStats_list_studies

  • Type: GWASSumStatsTool

  • Description: List studies in the EBI GWAS Catalog, newest API (v2). Returns the study accession with its reported trait, mapped EFO traits, PubMed id, first author, publication date and association count. Use the accession with GWASSumStats_get_region_associations’ FTP pointer to fetch that study’s full summary statistics.

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)