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tooluniverse-population-genetics-1000genomes

Query 1000 Genomes populations, samples, and data collections for ancestry-aware genetic analysis.

1.7k|254|Updated Mar 3, 2025
Search Tags:#gwas#ancestry#allele frequency#population genetics#1000 genomes#population stratification#igsr
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-population-genetics-1000genomes
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-population-genetics-1000genomes
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-population-genetics-1000genomes
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-population-genetics-1000genomes

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Researchers studying population genetics need structured access to 1000 Genomes Project (IGSR) data—population codes, sample metadata, and data collections—combined with GWAS context to perform ancestry-stratified analyses without manually navigating the IGSR portal.

Core Features & Use Cases

  • Population and Superpopulation Search: Search 1000 Genomes populations by superpopulation code (AFR/AMR/EAS/EUR/SAS) or free-text name, returning sample counts, coordinates, and ancestry labels.
  • Sample and Collection Lookup: Retrieve samples by population code (e.g., YRI, GBR), sample name (e.g., NA12878), or data collection (e.g., 30x high-coverage on GRCh38), and list all 18 available data collections.
  • GWAS Integration for Stratification: Cross-reference GWAS associations, trait variants (by EFO ID), and gene-mapped SNPs with population data to assess population-specific effects.
  • Use Case: To investigate whether a type 2 diabetes GWAS hit in TCF7L2 shows population-specific effects, list EUR populations, pull YRI samples for comparison, retrieve TCF7L2 GWAS SNPs, and compute allele frequency differences across superpopulations in Python.

Quick Start

List all African superpopulation populations in the 1000 Genomes Project and find samples from the YRI population.

Frequently Asked Questions about tooluniverse-population-genetics-1000genomes

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I find populations in the 1000 Genomes Project by ancestry?▼

Use IGSR_search_populations with a superpopulation code (AFR, AMR, EAS, EUR, or SAS) to list matching populations, or pass a free-text query like "Yoruba". Results include population codes, sample counts, and geographic coordinates.

How to look up 1000 Genomes samples from a specific population?▼

Call IGSR_search_samples with a population code such as YRI, GBR, or CHB to retrieve sample names, sex, biosample IDs, and associated data collections. Note that this parameter takes a population code, not a superpopulation code.

What is the difference between 1000 Genomes and gnomAD for allele frequencies?▼

1000 Genomes covers about 2500 samples across 26 populations, giving limited precision for rare variants (AF < 0.01). gnomAD has different sample composition and much larger cohorts, so use a gnomAD-based skill for reliable rare-variant frequency estimates.

Can I combine 1000 Genomes data with GWAS results?▼

Yes. Use gwas_search_associations, gwas_get_variants_for_trait (by EFO ID), or gwas_get_snps_for_gene to retrieve GWAS hits, then cross-reference with population data for stratification analysis and population-specific effect assessment.

What are the limitations of 1000 Genomes population data?▼

The dataset has roughly 2500 samples across 26 populations, so populations with fewer than 100 samples yield imprecise allele frequencies. It is also unsuitable for ClinVar/OMIM variant interpretation or GWAS fine-mapping, which need dedicated tools.

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