genome-compare

What problem does it solve?

Comparing personal genotype files to public references and estimating ancestry typically requires multiple bioinformatics tools, reference panels, and custom scripts; this skill collapses that workflow into a single reproducible pipeline that runs locally and preserves user privacy.

Core Features & Use Cases

• Pairwise IBS comparison: Compute identity-by-state (IBS) between a user's 23andMe genotype and George Church's public PGP-1 23andMe data, including SNP overlap counts and concordance.
• Per-chromosome breakdown: Report IBS statistics and overlap counts for each chromosome with visual summaries.
• Ancestry estimation: Estimate continental ancestry proportions (AFR, EUR, EAS, SAS, AMR) using an EM admixture algorithm on ancestry-informative markers (AIMs).
• Reproducible reporting: Produce a markdown report, structured JSON results, figures, and reproducibility bundle (commands and checksums) for auditability.
• Use Case: Rapidly assess how similar your 23andMe data is to a public reference and obtain an interpretable ancestry composition for research or demo purposes.

Quick Start

Compare my 23andMe file to George Church's reference and generate a reproducible report with IBS metrics, per-chromosome plots, and ancestry estimates.