Igsr Tools#

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

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

Available Tools#

IGSR_list_data_collections (Type: IGSRTool)#

List available data collections from IGSR. Results are recoverably paginated: start with offset=0…

IGSR_list_data_collections tool specification

Tool Information:

  • Name: IGSR_list_data_collections

  • Type: IGSRTool

  • Description: List available data collections from IGSR. Results are recoverably paginated: start with offset=0 and continue with next_offset while has_more is true. Returns collection codes, titles, sample/population counts, and available data types.

Parameters:

  • operation (string) (optional) Operation type (fixed: list_data_collections).

  • limit (integer) (optional) Results per page (1-500). The IGSR server’s real maximum is 500; invalid values return an error rather than being silently clamped.

  • offset (integer) (optional) Zero-based result offset. Continue with next_offset while has_more is true.

Example Usage:

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

IGSR_search_populations (Type: IGSRTool)#

Search 1000 Genomes Project populations from IGSR. Results are recoverably paginated: start with …

IGSR_search_populations tool specification

Tool Information:

  • Name: IGSR_search_populations

  • Type: IGSRTool

  • Description: Search 1000 Genomes Project populations from IGSR. Results are recoverably paginated: start with offset=0 and continue with next_offset while has_more is true. Pagination is applied after the superpopulation filter. Returns population codes, names, coordinates, sample counts, and superpopulation assignments.

Parameters:

  • operation (string) (optional) Operation type (fixed: search_populations).

  • superpopulation ([‘string’, ‘null’]) (optional) Filter by superpopulation code: AFR (African), AMR (Admixed American), EAS (East Asian), EUR (European), SAS (South Asian). Leave empty for all.

  • query ([‘string’, ‘null’]) (optional) Free-text search query to find populations by name or description (e.g., ‘Chinese’, ‘Yoruba’, ‘British’).

  • limit (integer) (optional) Results per page (1-500). The IGSR server’s real maximum is 500; invalid values return an error rather than being silently clamped.

  • offset (integer) (optional) Zero-based result offset. Continue with next_offset while has_more is true.

Example Usage:

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

IGSR_search_samples (Type: IGSRTool)#

Search samples from the 1000 Genomes Project by population, data collection, or sample name. Resu…

IGSR_search_samples tool specification

Tool Information:

  • Name: IGSR_search_samples

  • Type: IGSRTool

  • Description: Search samples from the 1000 Genomes Project by population, data collection, or sample name. Results are recoverably paginated: start with offset=0 and continue with next_offset while has_more is true. Returns sample names, sex, BioSample IDs, population assignments, and available data collections.

Parameters:

  • operation (string) (optional) Operation type (fixed: search_samples).

  • population ([‘string’, ‘null’]) (optional) Filter by population code (e.g., ‘CHB’, ‘YRI’, ‘GBR’, ‘CEU’). Use IGSR_search_populations to find valid codes.

  • data_collection ([‘string’, ‘null’]) (optional) Filter by data collection title (e.g., ‘1000 Genomes 30x on GRCh38’, ‘1000 Genomes on GRCh38’).

  • sample_name ([‘string’, ‘null’]) (optional) Look up specific sample by name (e.g., ‘HG00096’, ‘NA12878’).

  • limit (integer) (optional) Results per page (1-500). The IGSR server’s real maximum is 500; invalid values return an error rather than being silently clamped.

  • offset (integer) (optional) Zero-based result offset. Continue with next_offset while has_more is true.

Example Usage:

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