A procedure for checking and cataloguing VCF or BCF files, formats that store genetic variants. It records file hashes, sample names, and header details before later analysis without changing the original files.

Use it when receiving VCF, compressed VCF, or BCF files to identify their type, check indexes, inventory samples and metadata, and create run and sample summary files.

It creates a trustworthy record of what the input contains and catches problems such as malformed headers, missing indexes, or missing samples early. It avoids guessing important metadata when the evidence is weak.

How 45ck/open-genome-agent configures Claude Code and Codex

Reuse

Borrowing it

Nothing to install: this file belongs to 45ck/open-genome-agent. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/45ck/open-genome-agent/main/.agents/skills/ingest-vcf/SKILL.md

Clone the repo

git clone --depth 1 https://github.com/45ck/open-genome-agent

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/45ck/open-genome-agent/ingest-vcf/github.svg)](https://agentmods.dev/skills/45ck/open-genome-agent/ingest-vcf)

Your own site

<a href="https://agentmods.dev/skills/45ck/open-genome-agent/ingest-vcf"><img src="https://agentmods.dev/badge/skills/45ck/open-genome-agent/ingest-vcf/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/45ck/open-genome-agent/ingest-vcf"><img src="https://agentmods.dev/badge/skills/45ck/open-genome-agent/ingest-vcf.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 36 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 349 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	$0.00036	$0.00349
Opus 5	$0.00018	$0.00175
Sonnet 5	$0.00007	$0.00070
Haiku 4.5	$0.00004	$0.00035

Measured 9d ago against content hash 4c6a8a25595c, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

ingest-vcf 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 9d 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.

.agents/skills/ingest-vcf/SKILL.md · 48 lines

What it actually says

Ingest VCF

Validate and inventory VCF or BCF input files before downstream analysis. Use when a user provides a genome variant file or asks what data is inside it.

When to use

a VCF, VCF.GZ, BCF, TBI, or CSI file arrives
you need sample names, header metadata, or file hashes

Do not use when

the workflow starts from FASTQ only

Expected outputs

run_manifest.json
sample_summary.json

Goal

Create the first trustworthy manifest for a supplied VCF/BCF input.

Procedure

Identify the file kind: vcf, vcf.gz, or bcf.
Check for the expected index (.tbi or .csi) where relevant.
Extract sample names and header metadata without modifying the raw input.
Hash the input files and record them in run_manifest.json.
Create a minimal sample_summary.json with unresolved fields set to null.

Guardrails

Never rewrite the source file in place.
Do not guess the reference build from chromosome names alone if the evidence is weak.
Multi-sample files require explicit sample-selection logic.

Escalate when

the file has no samples
the header is malformed
the file is compressed but unindexed

References

See references/README.md for durable notes and scripts/ for deterministic helpers.

Files

What ships with it

2 files 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.

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.

9d ago First seen · 48 lines · 36 tokens per session scan A 4c6a8a25595c

Subscribe to this mod's changes

ingest-vcf is a skill published in the GitHub repository 45ck/open-genome-agent (4 stars, last pushed 2mo ago), licensed MIT. It adds 36 tokens to every session and 349 once invoked, about $0.0002 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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open-genome-agent: Skill for Claude Code