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Agent skill

Claw Ancestry Pca

by ClawBio in ClawBio/ClawBio

Ancestry decomposition PCA against the Simons Genome Diversity Project

MITAuto-check passedResearch & Science

Install Claw Ancestry Pca

skills CLI
$ npx skills add ClawBio/ClawBio --skill claw-ancestry-pca -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install ClawBio/ClawBio claw-ancestry-pca --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/claw-ancestry-pca .claude/skills/claw-ancestry-pca && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
claw-ancestry-pca
GitHub stars
1.2k
Used in
3 other repos
Token cost
~1.2k tokens
SKILL.md length
402 words
Files
4
Skills in repo
104
Repo updated
First seen
Licence
MIT

At a glance

Ancestry decomposition PCA against the Simons Genome Diversity Project

  • Works in 7 steps: Takes your VCF + population map as input → Finds common variants between your… → Runs PLINK PCA on the merged dataset → …
  • Tasks that involve Bioinformatics
  • SKILL.md covers What it does, Why this exists, Reference Panel and Usage, plus 3 more sections
  • Runs Python scripts from its folder; calls python

What it does

Claw Ancestry Pca is an agent skill from ClawBio/ClawBio. Ancestry decomposition PCA against the Simons Genome Diversity Project

Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `ancestry_pca.py`, `tests/__init__.py` and `tests/test_ancestry_pca.py`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

  • Tasks that involve Bioinformatics

Example prompts

  • “/claw-ancestry-pca”

Requirements

  • Python 3

Workflow steps

7 steps, taken from the first numbered list in SKILL.md.

  1. Takes your VCF + population map as input
  2. Finds common variants between your cohort and the SGDP reference panel (bundled)
  3. Runs PLINK PCA on the merged dataset
  4. Separates your cohort from SGDP reference samples
  5. Matches SGDP samples to their population labels (164 populations)
  6. Generates a publication-quality multi-panel figure
  7. Produces a markdown report with variance explained, population assignments, and reproducibility bundle

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships script files (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Claw Ancestry Pca loads about 1.2k tokens when it runs. Until then it costs about 22 tokens; SKILL.md has 402 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~22
When it runs · the whole SKILL.md, loaded when a task matches
~1.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 402 words, ~1,242 tokens.

Download SKILL.mdSave it as .claude/skills/claw-ancestry-pca/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
claw-ancestry-pca
description
Ancestry decomposition PCA against the Simons Genome Diversity Project
license
MIT
metadata.version
0.1.0
metadata.author
Manuel Corpas
metadata.tags
population-genetics, PCA, ancestry, SGDP, global-diversity

🦖 Ancestry Decomposition PCA

Place your study cohort in global genetic context by computing a joint PCA against the Simons Genome Diversity Project (SGDP) — 345 samples from 164 populations spanning every inhabited continent.

What it does

  1. Takes your VCF + population map as input
  2. Finds common variants between your cohort and the SGDP reference panel (bundled)
  3. Runs PLINK PCA on the merged dataset
  4. Separates your cohort from SGDP reference samples
  5. Matches SGDP samples to their population labels (164 populations)
  6. Generates a publication-quality multi-panel figure:
    • Panel A: PC1 vs PC2 — main population structure of your cohort
    • Panel B: PC3 vs PC2 with regional groupings and confidence ellipses
    • Panel C: PC3 vs PC1 with language/cultural groupings
    • Panel D: Global context — your samples (circles) vs SGDP (triangles)
  7. Produces a markdown report with variance explained, population assignments, and reproducibility bundle

Why this exists

If you ask ChatGPT to "run a PCA against a global reference panel," it will:

  • Not know which reference panel to use
  • Hallucinate PLINK flags for merging datasets with different variant sets
  • Skip IBD removal (related individuals distort PCA)
  • Not normalise contig names between your VCF and the reference
  • Produce a single scatter plot with no population labels

This skill encodes the correct methodological decisions:

  • Uses SGDP (the gold-standard reference for global diversity)
  • Handles contig normalisation (chr1 vs 1)
  • Filters to common biallelic SNPs shared between datasets
  • Removes related individuals via IBD checks
  • Produces publication-quality multi-panel figures with confidence ellipses
  • Differentiates your samples (circles) from reference (triangles)
Show full SKILL.md (151 more words)Show less

Reference Panel

The skill bundles the SGDP v4 dataset (Mallick et al., 2016, Nature):

  • 345 samples from 164 populations
  • Whole-genome sequencing at high coverage
  • MAF > 0.1% filter applied
  • Populations span: Africa, Americas, Central/South Asia, East Asia, Europe, Middle East, Oceania

Usage

bash
python ancestry_pca.py \
    --vcf your_cohort.vcf.gz \
    --pop-map your_populations.tsv \
    --output ancestry_report
Demo (works out of the box)
bash
python ancestry_pca.py --demo --output demo_report

The demo uses pre-computed PCA results from the Peruvian Genome Project (736 samples, 28 populations) and generates the full 4-panel figure instantly.

Example Output

Ancestry Decomposition PCA
==========================
Cohort: 736 samples, 28 populations
Reference: SGDP (345 samples, 164 populations)
Common variants: 42,831 biallelic SNPs

Variance explained:
  PC1: 51.44%  PC2: 21.70%  PC3: 6.70%

Panel D — Global Context:
  Cohort samples cluster between European and East Asian
  reference populations, with Amazonian groups showing
  distinct positioning from Highland and Coastal groups.

Figures saved to: ancestry_report/
  Figure3_PCA_composite.png (300 dpi)
  Figure3_PCA_composite.pdf (vector)

Reproducibility:
  commands.sh | environment.yml | checksums.sha256

Interpretation Guide

  • PC1 typically captures the largest axis of global differentiation (often Africa vs non-Africa)
  • PC2 separates major continental groups (Europe, East Asia, Americas)
  • PC3 often reveals finer substructure within continental groups
  • Confidence ellipses show 2.5 standard deviations around each population cluster
  • Your samples shown as circles, SGDP reference as triangles

Citation

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

© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files in skills/claw-ancestry-pca of ClawBio/ClawBio.

  • SKILL.md
  • ancestry_pca.py
  • tests/__init__.py
  • tests/test_ancestry_pca.py

Open the folder on GitHubat commit dece754

Used in 3 other repositories

We found 3 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 3 other GitHub owners. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Claw Ancestry Pca next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Claw Ancestry Pca compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Claw Ancestry Pca this skillClawBio/ClawBio1.2k3 repos~1.2kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

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Categories

Questions about Claw Ancestry Pca

What does Claw Ancestry Pca do?

Ancestry decomposition PCA against the Simons Genome Diversity Project. Claw Ancestry Pca is an agent skill from ClawBio/ClawBio.

When should I use Claw Ancestry Pca?

Claw Ancestry Pca fits situations like: tasks that involve Bioinformatics.

How do I install Claw Ancestry Pca in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill claw-ancestry-pca -a claude-code`. Or copy the skill folder (skills/claw-ancestry-pca in ClawBio/ClawBio) into .claude/skills/claw-ancestry-pca in your project. Claude Code loads it when a task matches its description.

How do I install Claw Ancestry Pca in Codex?

Run `npx skills add ClawBio/ClawBio --skill claw-ancestry-pca -a codex`. Or copy the skill folder (skills/claw-ancestry-pca in ClawBio/ClawBio) into .agents/skills/claw-ancestry-pca in your project. Codex loads it when a task matches its description.

Can I use Claw Ancestry Pca in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill claw-ancestry-pca -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/claw-ancestry-pca, .gemini/skills/claw-ancestry-pca, .github/skills/claw-ancestry-pca and .opencode/skills/claw-ancestry-pca in your project.

What does Claw Ancestry Pca need to run?

Going by SKILL.md and its folder, Claw Ancestry Pca needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Claw Ancestry Pca access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Claw Ancestry Pca safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Claw Ancestry Pca use?

Claw Ancestry Pca is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Claw Ancestry Pca use?

About 1.2k tokens (SKILL.md is roughly 5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Claw Ancestry Pca?

Skills that share tags, products or a category with Claw Ancestry Pca: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Claw Ancestry Pca?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,155 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 9, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.