Gwas Tools

Configuration File: gwas_tools.json Tool Type: Local Tools Count: 12

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

Available Tools

gwas_get_association_by_id (Type: GWASAssociationByID)

Get a specific GWAS association by its unique identifier.

gwas_get_association_by_id tool specification

Tool Information:

• Name: gwas_get_association_by_id

• Type: GWASAssociationByID

• Description: Get a specific GWAS association by its unique identifier.

Parameters:

• association_id (string) (required) GWAS association identifier

Example Usage:

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

gwas_get_associations_for_snp (Type: GWASAssociationsForSNP)

Get all associations for a specific SNP with optional sorting.

gwas_get_associations_for_snp tool specification

Tool Information:

• Name: gwas_get_associations_for_snp

• Type: GWASAssociationsForSNP

• Description: Get all associations for a specific SNP with optional sorting.

Parameters:

• rs_id (string) (required) dbSNP rs identifier

• sort (string) (optional) Sort field (e.g., ‘p_value’, ‘or_value’)

• direction (string) (optional) Sort direction (‘asc’ or ‘desc’)

• size (integer) (optional) Number of results to return per page

• page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_get_associations_for_study (Type: GWASAssociationsForStudy)

Get all associations for a specific study, sorted by p-value.

gwas_get_associations_for_study tool specification

Tool Information:

• Name: gwas_get_associations_for_study

• Type: GWASAssociationsForStudy

• Description: Get all associations for a specific study, sorted by p-value.

Parameters:

• accession_id (string) (required) Study accession identifier

• size (integer) (optional) Number of results to return per page

• page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_get_associations_for_trait (Type: GWASAssociationsForTrait)

Get all associations for a specific trait, sorted by p-value (most significant first).

gwas_get_associations_for_trait tool specification

Tool Information:

• Name: gwas_get_associations_for_trait

• Type: GWASAssociationsForTrait

• Description: Get all associations for a specific trait, sorted by p-value (most significant first).

Parameters:

• efo_trait (string) (required) EFO trait identifier or name

• size (integer) (optional) Number of results to return per page

• page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_get_snp_by_id (Type: GWASSNPByID)

Get a specific GWAS SNP by its rs ID.

gwas_get_snp_by_id tool specification

Tool Information:

• Name: gwas_get_snp_by_id

• Type: GWASSNPByID

• Description: Get a specific GWAS SNP by its rs ID.

Parameters:

• rs_id (string) (required) dbSNP rs identifier

Example Usage:

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

gwas_get_snps_for_gene (Type: GWASSNPsForGene)

Get all SNPs mapped to a specific gene.

gwas_get_snps_for_gene tool specification

Tool Information:

• Name: gwas_get_snps_for_gene

• Type: GWASSNPsForGene

• Description: Get all SNPs mapped to a specific gene.

Parameters:

• mapped_gene (string) (required) Gene name or symbol

• size (integer) (optional) Number of results to return per page

• page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_get_studies_for_trait (Type: GWASStudiesForTrait)

Get studies for a specific trait with optional filters for cohort, GxE interactions, and summary …

gwas_get_studies_for_trait tool specification

Tool Information:

• Name: gwas_get_studies_for_trait

• Type: GWASStudiesForTrait

• Description: Get studies for a specific trait with optional filters for cohort, GxE interactions, and summary statistics.

Parameters:

• efo_trait (string) (optional) EFO trait identifier or name

• disease_trait (string) (optional) Disease trait name

• cohort (string) (optional) Cohort name (e.g., ‘UKB’ for UK Biobank)

• gxe (boolean) (optional) Filter for Gene-by-Environment interaction studies

• full_pvalue_set (boolean) (optional) Filter for studies with full summary statistics

• size (integer) (optional) Number of results to return per page

• page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_get_study_by_id (Type: GWASStudyByID)

Get a specific GWAS study by its unique identifier.

gwas_get_study_by_id tool specification

Tool Information:

• Name: gwas_get_study_by_id

• Type: GWASStudyByID

• Description: Get a specific GWAS study by its unique identifier.

Parameters:

• study_id (string) (required) GWAS study identifier

Example Usage:

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

gwas_get_variants_for_trait (Type: GWASVariantsForTrait)

Get all variants associated with a specific trait with pagination support.

gwas_get_variants_for_trait tool specification

Tool Information:

• Name: gwas_get_variants_for_trait

• Type: GWASVariantsForTrait

• Description: Get all variants associated with a specific trait with pagination support.

Parameters:

• efo_trait (string) (required) EFO trait identifier or name

• size (integer) (optional) Number of results to return per page

• page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_search_associations (Type: GWASAssociationSearch)

Search for GWAS associations by various criteria including EFO trait, rs ID, accession ID, with s…

gwas_search_associations tool specification

Tool Information:

• Name: gwas_search_associations

• Type: GWASAssociationSearch

• Description: Search for GWAS associations by various criteria including EFO trait, rs ID, accession ID, with sorting and pagination support.

Parameters:

• efo_trait (string) (optional) EFO trait identifier or name

• rs_id (string) (optional) dbSNP rs identifier

• accession_id (string) (optional) Study accession identifier

• sort (string) (optional) Sort field (e.g., ‘p_value’, ‘or_value’)

• direction (string) (optional) Sort direction (‘asc’ or ‘desc’)

• size (integer) (optional) Number of results to return

• page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_search_snps (Type: GWASSNPSearch)

Search for GWAS single nucleotide polymorphisms (SNPs) by rs ID or mapped gene.

gwas_search_snps tool specification

Tool Information:

• Name: gwas_search_snps

• Type: GWASSNPSearch

• Description: Search for GWAS single nucleotide polymorphisms (SNPs) by rs ID or mapped gene.

Parameters:

• rs_id (string) (optional) dbSNP rs identifier

• mapped_gene (string) (optional) Gene name or symbol

• size (integer) (optional) Number of results to return

• page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_search_studies (Type: GWASStudySearch)

Search for GWAS studies by various criteria including EFO trait, disease trait, cohort, GxE inter…

gwas_search_studies tool specification

Tool Information:

• Name: gwas_search_studies

• Type: GWASStudySearch

• Description: Search for GWAS studies by various criteria including EFO trait, disease trait, cohort, GxE interactions, and summary statistics availability.

Parameters:

• efo_trait (string) (optional) EFO trait identifier or name

• disease_trait (string) (optional) Disease trait name

• cohort (string) (optional) Cohort name (e.g., ‘UKB’ for UK Biobank)

• gxe (boolean) (optional) Filter for Gene-by-Environment interaction studies

• full_pvalue_set (boolean) (optional) Filter for studies with full summary statistics

• size (integer) (optional) Number of results to return

• page (integer) (optional) Page number for pagination

Example Usage:

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

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