tooluniverse-population-genetics-1000genomes

COMPUTE, DON'T DESCRIBE

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

Population Genetics with 1000 Genomes (IGSR)

Use IGSR tools to search 1000 Genomes populations and samples, explore data collections, and combine with GWAS tools for population-stratified analysis.

When to Use

• "List all African (AFR) populations in the 1000 Genomes Project"
• "Find samples from the YRI (Yoruba) population"
• "What 1000 Genomes data collections are available?"
• "Which GWAS SNPs for type 2 diabetes have population-specific effects?"
• "Find all SNPs mapped to TCF7L2 in GWAS studies"

NOT for (use other skills instead)

• Allele frequencies from gnomAD -> Use tooluniverse-population-genetics
• ClinVar / OMIM variant interpretation -> Use tooluniverse-variant-interpretation
• GWAS fine-mapping -> Use tooluniverse-gwas-finemapping

---

Phase 1: Search 1000 Genomes Populations

IGSR_search_populations: superpopulation (string/null, one of AFR/AMR/EAS/EUR/SAS), query (string/null, free-text search by name), limit (int). Returns {status, data: {total, populations: [{code, name, description, sample_count, superpopulation_code, superpopulation_name, latitude, longitude}]}, metadata: {source, filter_superpopulation, filter_query}}.

Superpopulation codes:

Code	Ancestry
AFR	African
AMR	Admixed American
EAS	East Asian
EUR	European
SAS	South Asian

// List all AFR populations
{"superpopulation": "AFR", "limit": 10}

// Search by name (free-text)
{"query": "Yoruba", "limit": 5}

// List all populations
{"limit": 26}

Response example:

{
  "status": "success",
  "data": {
    "total": 3,
    "populations": [
      {"code": "YRI", "name": "Yoruba", "description": "Yoruba in Ibadan, Nigeria",
       "sample_count": 188, "superpopulation_code": "AFR", "superpopulation_name": "African Ancestry"}
    ]
  }
}