What is gigwa-diversity-report?

A read-only report for a Gigwa variant set, where a variant set is a collection of genetic changes from a study. It summarises genetic diversity, population structure, relatedness, and optionally differences between defined groups.

Use it to calculate diversity statistics, principal component analysis (PCA, a way to show sample patterns), clustering, kinship, a phylogenetic tree, and—when groups are supplied—group-level diversity and Fst.

It brings several common genetic analyses into one report, so you do not have to assemble results from separate checks. It helps explain whether samples are diverse, clustered, or closely related after quality control.

gigwa-diversity-report — Skill for Claude Code and Codex by gkanogiann

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 gkanogiannis/Gigwa-MCP --skill gigwa-diversity-report

Clone the repo

git clone --depth 1 https://github.com/gkanogiannis/Gigwa-MCP

Made for: Claude Code, Codex.

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gkanogiannis/gigwa-mcp/gigwa-diversity-report/github.svg)](https://agentmods.dev/skills/gkanogiannis/gigwa-mcp/gigwa-diversity-report)

Your own site

<a href="https://agentmods.dev/skills/gkanogiannis/gigwa-mcp/gigwa-diversity-report"><img src="https://agentmods.dev/badge/skills/gkanogiannis/gigwa-mcp/gigwa-diversity-report/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/gkanogiannis/gigwa-mcp/gigwa-diversity-report"><img src="https://agentmods.dev/badge/skills/gkanogiannis/gigwa-mcp/gigwa-diversity-report.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 204 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,339 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.

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.

Model	Per session	Once invoked
Fable 5.1	$0.00204	$0.01339
Opus 5	$0.00102	$0.00669
Sonnet 5	$0.00041	$0.00268
Haiku 4.5	$0.00020	$0.00134

Measured 11d ago against content hash e1cd2a29703d, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

gigwa-diversity-report 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 11d 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.

skills/gigwa-diversity-report/SKILL.md · 93 lines

How it starts

The opening of the file, as written. The whole thing — 93 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Gigwa diversity report

Overview

Characterise a variant set's genetic diversity, population structure and relatedness in one coherent report: dataset-wide summary statistics, PCA, structure clustering, a kinship matrix, a phylogenetic tree, and — when groups are defined — per-group diversity and Fst. All steps drive the gigwa-mcp MCP server's read-only diversity_* tools.

When to use

After QC passes for a run (see gigwa-qc-triage), when the user wants the biology: how diverse, how structured, how related.
You need a variant_set_db_id (MODULE§project§run) — get it from list_variant_sets() (or the gigwa-explore-instance skill).

Prerequisites and grouping

The gigwa-mcp server is connected; read-only, so anonymous access is fine.
Grouping is optional. To get per-group diversity and Fst, define groups one of two ways:
- a metadata TSV plus a group_column (rows keyed by id_column, default individual), or
- an explicit groups_json mapping (accepted by diversity_fst / diversity_by_group).
No groups → run the ungrouped core (steps 1–4) only.

Step-by-step workflow

Dataset summary — diversity_summary(variant_set_db_id): per-marker MAF, He, Ho, PIC and dataset means. This is the baseline everything else is read against.
Structure —
- diversity_pca(variant_set_db_id, n_components=10): variance explained + PC coordinates (pca_coords.csv). Pass metadata_tsv + group_column to colour/label PCs by group.
- diversity_structure(variant_set_db_id, k_min=2, k_max=10): PCA + K-means clustering with a suggested K.
Relatedness — diversity_kinship(variant_set_db_id, top_pairs=15): VanRaden genomic relationship matrix; report the closest pairs (possible clones/close relatives).
Tree — diversity_tree(variant_set_db_id, max_markers=5000): UPGMA dendrogram from IBS distance (tree.nwk).
Grouped (only if groups defined) —
- diversity_by_group(variant_set_db_id, metadata_tsv=…, group_column=…): per-population He/Ho/Fis/MAF and allelic richness.
- diversity_fst(variant_set_db_id, metadata_tsv=…, group_column=…): pairwise Weir and Cockerham Fst between groups.

Read the full file on GitHub · 93 lines

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

references/popgen-metrics.md 3.7 KB

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.

11d ago First seen · 93 lines · 204 tokens per session scan A e1cd2a29703d

Subscribe to this mod's changes

gigwa-diversity-report is a skill published in the GitHub repository gkanogiannis/Gigwa-MCP (0 stars, last pushed 2d ago), licensed Apache-2.0. It adds 204 tokens to every session and 1,339 once invoked, about $0.0010 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 2026-08-31.

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