Population Genetics Analysis

MC Strategy: Population genetics MC questions often test whether you know a specific theorem or result. COMPUTE the answer first (use popgen_calculator.py or write Python), then match to options. Don't try to reason about which option "sounds right."

Analyze population-level genetic variation, allele frequencies, GWAS associations, clinical significance, and evolutionary constraints using ToolUniverse tools.

When to Use

Activate this skill when the user asks about:

• Allele frequencies across populations (gnomAD, 1000 Genomes)
• GWAS associations for diseases/traits
• Clinical variant interpretation (ClinVar, VEP)
• Gene-level constraint metrics (pLI, LOEUF, o/e ratios)
• Selection, drift, linkage disequilibrium, or population structure
• Variant annotation and functional consequences

LOOK UP, DON'T GUESS

Query gnomAD/1000Genomes/GWAS Catalog FIRST for allele frequencies and associations. Preferred: use the PopGen_hwe_test, PopGen_fst, PopGen_inbreeding, and PopGen_haplotype_count tools for HWE, Fst, inbreeding, and haplotype calculations. Fallback: run popgen_calculator.py directly. For theoretical problems (delta-q, drift, LD decay), apply the formulas in the Theoretical Reasoning section below.