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.
curl -O https://raw.githubusercontent.com/45ck/open-genome-agent/main/.agents/skills/annotate-variants/SKILL.mdgit clone --depth 1 https://github.com/45ck/open-genome-agentWrote 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.
[](https://agentmods.dev/skills/45ck/open-genome-agent/annotate-variants)<a href="https://agentmods.dev/skills/45ck/open-genome-agent/annotate-variants"><img src="https://agentmods.dev/badge/skills/45ck/open-genome-agent/annotate-variants/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.
<a href="https://agentmods.dev/skills/45ck/open-genome-agent/annotate-variants"><img src="https://agentmods.dev/badge/skills/45ck/open-genome-agent/annotate-variants.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00032 | $0.00295 |
| Opus 5.5 | $0.00013 | $0.00118 |
| Sonnet 5.5 | $0.00006 | $0.00059 |
| Haiku 4.5 | $0.00003 | $0.00030 |
Grade A, and why
annotate-variants 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.
What it actually says
Annotate variants
Annotate variants with deterministic tools such as VEP and preserve exact tool versions and command provenance. Use after normalization and before prioritization.
When to use
- gene/transcript consequences are needed
- you need a structured annotation file for later ranking
Do not use when
- you only need simple file QC
Expected outputs
annotations.tsvtool_versions.jsoncommands.jsonl
Goal
Produce a structured annotation layer that downstream agents can rank and report.
Procedure
- Confirm build and normalization state first.
- Run the selected annotation tool with explicit version capture.
- Preserve raw command lines and output paths in
commands.jsonl. - Emit a stable tabular or JSON annotation artifact.
- Keep tool failures visible and non-silent.
Guardrails
- Annotation is not interpretation.
- Do not collapse multiple transcripts into a single unqualified claim.
- Record exact tool and cache versions when available.
Escalate when
- required annotation caches are missing
- reference build does not match tool expectations
- command output suggests truncation or partial failure
References
See references/README.md for durable notes and scripts/ for deterministic helpers.
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.
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 · 49 lines · 32 tokens per session scan A 6b424dab9085
annotate-variants is a skill published in the GitHub repository 45ck/open-genome-agent (4 stars, last pushed 4mo ago), licensed MIT. It adds 32 tokens to every session and 295 once invoked, about $0.0001 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.
Other skills, from other repositories
biomcp-research
Do biomedical literature and variant research with the BioMCP CLI, and file what you learn about the tool itself as issues in the biomcp repo.
genomics-cnv-calling
Load when calling CNV segments via CBS-style segmentation on a bin-level log2-ratio CSV from exome / WGS coverage — emits per-segment 5-class CN state (amplification / gain / neutral / loss / deepdeletion), per-chromosome summary, genome-fraction-altered. Skip when working with single-cell / spatial CNV (use…
genomics-epigenomics
Load when summarising a peak file (BED / narrowPeak) from ATAC-seq / ChIP-seq / CUT&Tag — peak count, width distribution, per-chromosome counts, score statistics. Skip when calling peaks from BAM (run MACS / Genrich externally first); working with single-cell ATAC (use scatac-preprocessing).
genomics-phasing
Load when summarising a phased VCF (output of WhatsHap / SHAPEIT5 / Eagle2) — phased fraction of het variants, phase-block N50, PS-field parsing, pipe-delimited genotype detection. Skip when the input is unphased (run a phaser first); calling small variants (use genomics-variant-calling).
genomics-qc
Load when running pre-alignment FASTQ quality control — Phred quality scores, Q20/Q30 rates, GC / N content, read-length distribution, adapter-contamination detection. Skip when working with already-aligned BAMs (use genomics-alignment); peak / variant files are the input (use the relevant downstream skill).
genomics-alignment
Load when computing alignment QC metrics (mapping rate, MAPQ distribution, insert size, duplicate rate, proper-pair rate) from a text SAM file produced by any short-/long-read aligner (BWA / Bowtie2 / Minimap2); convert a BAM with samtools view -h first. Skip when running the alignment step itself; only FASTQ-level QC…