claw-ancestry-pca

What problem does it solve?

This Skill places a study cohort into global genetic context by computing a joint PCA against a curated global reference panel and automating the complex preprocessing steps required for robust ancestry inference and reproducible reporting.

Core Features & Use Cases

• Reference-aware PCA: merges cohort VCFs with the Simons Genome Diversity Project (SGDP) reference panel to show global population structure.
• Robust preprocessing: performs contig name normalization, filters to shared biallelic SNPs, removes related individuals via IBD checks, and mean-imputes missing genotypes.
• Publication-ready outputs: produces a multi-panel PCA composite figure (PC1vPC2, PC2vPC3, PC1vPC3, scree), CSV tables of PC coordinates and variance, a markdown report with interpretation guidance, and a reproducibility bundle (commands, environment, checksums).
• Use Case: situate research participants on global ancestry axes, assign likely population labels for downstream analyses, and generate figures and reproducible artifacts for publications or quality control.

Quick Start

Run the ancestry PCA pipeline on your cohort VCF and population map and save the report to a results directory.