claw-ancestry-pca

claw-ancestry-pca is a skill for Claude Code from aAAaqwq/AGI-Super-Team. It costs 20 tokens per session (1,204 once invoked), scanned A, original, MIT.

A genetic ancestry analysis workflow that compares a study group with the Simons Genome Diversity Project, a reference collection of genomes from populations around the world. It uses shared genetic variants to run principal component analysis (PCA), a method for showing major patterns of genetic variation.

In plain words
What is it for?
Use it with a VCF file and population map to compare samples, assign reference population labels, create multi-panel figures, and generate a report.
Why use it?
It gives the study group a global reference for interpreting genetic structure instead of relying on an unspecified comparison set.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin. Also seen: built for openclaw.

Part of the agi-super-team plugin — 194 skills, 1 agent shipped together

Good fit Use it with a VCF file and population map to compare samples, assign reference population labels, create multi-panel figures, and generate a report.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/aaaaqwq/agi-super-team/claw-ancestry-pca
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add aAAaqwq/AGI-Super-Team --skill claw-ancestry-pca
Clone the repo
git clone --depth 1 https://github.com/aAAaqwq/AGI-Super-Team

Made for: Claude Code.

Or install agi-super-team, the plugin that ships this one along with the rest of its 194 skills, 1 agent.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for claw-ancestry-pca

README.md
[![agentmods](https://agentmods.dev/badge/skills/aaaaqwq/agi-super-team/claw-ancestry-pca/github.svg)](https://agentmods.dev/skills/aaaaqwq/agi-super-team/claw-ancestry-pca)
Your own site
<a href="https://agentmods.dev/skills/aaaaqwq/agi-super-team/claw-ancestry-pca"><img src="https://agentmods.dev/badge/skills/aaaaqwq/agi-super-team/claw-ancestry-pca/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for claw-ancestry-pca

Your own site · 80×15
<a href="https://agentmods.dev/skills/aaaaqwq/agi-super-team/claw-ancestry-pca"><img src="https://agentmods.dev/badge/skills/aaaaqwq/agi-super-team/claw-ancestry-pca.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 20 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,204 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00020 $0.01204
Opus 5 $0.00010 $0.00602
Sonnet 5 $0.00004 $0.00241
Haiku 4.5 $0.00002 $0.00120

Measured 6d ago against content hash cc8199935491, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-11, from the pricing page.

Security

Grade A, and why

claw-ancestry-pca scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

skills/claw-ancestry-pca/SKILL.md · 146 lines

How it starts

The opening of the file, as written. The whole thing — 146 lines — stays where its author put it; the contents beside it link to each section on GitHub.

🦖 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)

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

Read the full file on GitHub · 146 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 6d ago First seen · 146 lines · 20 tokens per session scan A cc8199935491

Subscribe to this mod's changes

claw-ancestry-pca is a skill published in the GitHub repository aAAaqwq/AGI-Super-Team (91 stars, last pushed yesterday), licensed MIT. It adds 20 tokens to every session and 1,204 once invoked, about $0.0001 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-05.

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