What is gigwa-region-scan?

A tool for examining variation in one chromosome or other genomic region within a stored set of genetic variants. It reports what variants occur there and how common, diverse, or complete the data is.

It helps count and search variants, compare common and rare variants, measure local genetic diversity, and check data quality for a chromosome or coordinate window in Gigwa.

It avoids searching an entire variant collection when the question concerns only a small coordinate range, while reducing errors caused by different region formats.

gigwa-region-scan — Skill for Claude Code and Codex by gkanogiannis

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-region-scan

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-region-scan/github.svg)](https://agentmods.dev/skills/gkanogiannis/gigwa-mcp/gigwa-region-scan)

Your own site

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

Per session 217 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,182 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	$0.00217	$0.01182
Opus 5.5	$0.00087	$0.00473
Sonnet 5.5	$0.00043	$0.00236
Haiku 4.5	$0.00022	$0.00118

Measured 2mo ago against content hash 4324e166c890, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

gigwa-region-scan 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 2mo 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-region-scan/SKILL.md · 83 lines

How it starts

The opening of the file, as written. The whole thing — 83 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Gigwa region scan

Overview

Zoom into one genomic window of a variant set and report its variant density, common vs rare composition, and local diversity/quality. Drives the gigwa-mcp MCP server's search, diversity and QC tools against a single region.

When to use

A user names a chromosome/contig (chr1) or a coordinate range (chr1:1000000-2000000) and wants to know what's there.
You need a variant_set_db_id (MODULE§project§run) — from list_variant_sets() or the gigwa-explore-instance skill.

Region syntax — the two interfaces (important)

The tools take the interval two different ways. Get this right or the filters silently apply to the whole set:

Tool(s)	How to pass the window
`count_variants`, `search_variants`	split into `reference_name`, `start`, `end` (there is no `region` param)
`diversity_summary`, `qc_call_rate`	one `region` string: `"chrom"` or `"chrom:start-end"`

Mapping example for chr1:1000000-2000000:

search/count → reference_name="chr1", start=1000000, end=2000000
diversity/QC → region="chr1:1000000-2000000"

Coordinates are 1-based inclusive. A whole chromosome is reference_name="chr1" (no start/end) or region="chr1".

Step-by-step workflow

Validate the contig — list_sequences(variant_set_db_id) to confirm the exact reference_name exists (names must match the run's contigs).
Count —
- count_variants(variant_set_db_id, reference_name, start, end) — total variants in the window.
- count_variants(variant_set_db_id, reference_name, start, end, min_maf=0.05) — again, restricted to common variants; the gap = rare/low-frequency variants.
List — search_variants(variant_set_db_id, reference_name, start, end) writes the matching variants to variant_search.csv (respects the same MAF/missingness filters; capped by max_variants=100000).
Characterise the window (note the region= string form):
- diversity_summary(variant_set_db_id, region="chr1:1000000-2000000")
- qc_call_rate(variant_set_db_id, region="chr1:1000000-2000000")
Report variant density (per bp / per window), common-vs-rare split, and local diversity/call-rate.

Read the full file on GitHub · 83 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/region-queries.md 2.5 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.

2mo ago First seen · 83 lines · 217 tokens per session scan A 4324e166c890

Subscribe to this mod's changes

gigwa-region-scan is a skill published in the GitHub repository gkanogiannis/Gigwa-MCP (0 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 217 tokens to every session and 1,182 once invoked, about $0.0009 per session on Opus 5.5. 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.

Scientific

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