Claw Ancestry Pca

🦖 Ancestry Decomposition PCA

Compute a principal-component decomposition of your own cohort's genotypes from a VCF, coloured by population label, and write a report plus a 4-panel figure.

What it does

1. Takes your VCF + optional population map as input
2. Parses genotypes into a sample × variant matrix (0/1/2, -1 missing)
3. Mean-imputes missing genotypes per variant
4. Runs sklearn.decomposition.PCA on that matrix
5. Generates a 4-panel figure:
   • Panel A: PC1 vs PC2
   • Panel B: PC2 vs PC3
   • Panel C: PC1 vs PC3
   • Panel D: Scree plot — per-PC and cumulative variance explained
6. Produces report.md, result.json, and tables/ with PC coordinates and variance explained

Scope and limits

Read these before interpreting the output.

• Single cohort only. No reference panel ships with this skill and none is downloaded. Samples are not placed in global context, and the figure has no reference-vs-cohort marker distinction and no confidence ellipses.
• No PLINK, no bcftools. The script never shells out; PCA is computed in-process with scikit-learn.
• No Patterson standardisation. Genotypes are not divided by sqrt(p(1-p)), so PCs are not on the standard population-genetics scale.
• No LD pruning and no relatedness (IBD) filtering. Prune and remove related individuals upstream — otherwise PCs will track LD blocks and cryptic relatedness rather than ancestry.
• No contig-name normalisation. Supply one consistent naming scheme (chr1 or 1).

Requirements

The script imports clawbio.common (VCF parsing, checksums, report helpers) from three directory levels above itself, and reads its demo data from examples/. Both come from https://github.com/ClawBio/ClawBio — run this skill from inside a ClawBio checkout, or put clawbio/ and examples/ on that path. Without them the script fails at import.

Usage

python ancestry_pca.py \
    --input your_cohort.vcf.gz \
    --pop-map your_populations.csv \
    --output ancestry_report

Omit --output for a text summary on stdout. --pop-map is a CSV/TSV with sample_id and population columns; unmapped samples are labelled UNKNOWN.

Demo

python ancestry_pca.py --demo --output demo_report

The demo runs on examples/demo_populations.vcf from the ClawBio checkout — 50 samples, 500 variants, 5 population labels.

Example Output

Verbatim from --demo:

Parsing VCF...
  50 samples, 500 variants
  Populations: AFR (n=8), AMR (n=5), EAS (n=7), EUR (n=22), SAS (n=8)
Computing PCA (10 components)...
  PC1: 7.6%  PC2: 4.9%
Generating figures...
Generating report...

Done.
  Report: demo_report/report.md
  Figures: demo_report/figures

Written under the output directory:

report.md
result.json
figures/pca_composite.png
tables/pc_coordinates.csv
tables/variance_explained.csv

Interpretation Guide

• PC1/PC2 capture the largest axes of variation in the supplied cohort — with no reference panel these are cohort-relative, not global, axes
• Variance explained is low and spread across many PCs when the cohort is genetically homogeneous; check Panel D before reading structure into A–C
• Unstandardised, unpruned PCs are sensitive to LD blocks and relatedness — confirm both were handled upstream before calling a cluster "ancestry"

Citation

If you use this skill in a publication, please cite:

• Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio