Gwas Tools ========== **Configuration File**: ``gwas_tools.json`` **Tool Type**: Local **Tools Count**: 13 This page contains all tools defined in the ``gwas_tools.json`` configuration file. Available Tools --------------- **GWAS_search_associations_by_gene** (Type: GWASGeneSearch) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields). .. dropdown:: GWAS_search_associations_by_gene tool specification **Tool Information:** * **Name**: ``GWAS_search_associations_by_gene`` * **Type**: ``GWASGeneSearch`` * **Description**: Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields). **Parameters:** * ``gene_name`` (string) (required) Gene symbol (e.g., BRCA1). * ``size`` (integer) (optional) Max associations to return. **Example Usage:** .. code-block:: python query = { "name": "GWAS_search_associations_by_gene", "arguments": { "gene_name": "example_value" } } result = tu.run(query) **gwas_get_association_by_id** (Type: GWASAssociationByID) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Get a specific GWAS association by its unique identifier. .. dropdown:: 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:** .. code-block:: python 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. .. dropdown:: 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:** .. code-block:: python 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. .. dropdown:: 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:** .. code-block:: python 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). .. dropdown:: 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:** .. code-block:: python 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. .. dropdown:: 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:** .. code-block:: python 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. .. dropdown:: 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:** .. code-block:: python 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 ... .. dropdown:: 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:** .. code-block:: python 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. .. dropdown:: 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:** .. code-block:: python 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. .. dropdown:: 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:** .. code-block:: python 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... .. dropdown:: 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:** .. code-block:: python 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. .. dropdown:: 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:** .. code-block:: python 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... .. dropdown:: 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:** .. code-block:: python query = { "name": "gwas_search_studies", "arguments": { } } result = tu.run(query) Navigation ---------- * :doc:`tools_config_index` - Back to Tools Overview * :doc:`../guide/loading_tools` - Loading Local Tools