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.
npx skills add AndyZhuang/Opentest --skill tooluniverse-variant-analysisgit clone --depth 1 https://github.com/AndyZhuang/OpentestWrote 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/andyzhuang/opentest/tooluniverse-variant-analysis)<a href="https://agentmods.dev/skills/andyzhuang/opentest/tooluniverse-variant-analysis"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/tooluniverse-variant-analysis/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/andyzhuang/opentest/tooluniverse-variant-analysis"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/tooluniverse-variant-analysis.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 | $0.00238 | $0.04144 |
| Opus 5 | $0.00119 | $0.02072 |
| Sonnet 5 | $0.00048 | $0.00829 |
| Haiku 4.5 | $0.00024 | $0.00414 |
Grade A, and why
tooluniverse-variant-analysis 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 8d 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.
How it starts
The opening of the file, as written. The whole thing — 449 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Variant Analysis and Annotation
Production-ready VCF processing and variant annotation skill combining local bioinformatics computation with ToolUniverse database integration. Designed to answer bioinformatics analysis questions about VCF data, mutation classification, variant filtering, and clinical annotation.
When to Use This Skill
Triggers:
- User provides a VCF file (SNV/indel or SV) and asks questions about its contents
- Questions about variant allele frequency (VAF) filtering
- Mutation type classification queries (missense, nonsense, synonymous, etc.)
- Structural variant interpretation requests (deletions, duplications, CNVs)
- Variant annotation requests (ClinVar, gnomAD, CADD, dbSNP)
- CNV pathogenicity assessment using ClinGen dosage sensitivity
- Cohort comparison questions
- Population frequency filtering (SNVs or SVs)
- Intronic/intergenic variant filtering
- Gene dosage sensitivity queries
Example Questions:
- "What fraction of variants with VAF < 0.3 are annotated as missense mutations?"
- "After filtering intronic/intergenic variants, how many non-reference variants remain?"
- "What is the clinical significance of this deletion affecting BRCA1?"
- "Which dosage-sensitive genes overlap this 500kb duplication on chr17?"
- "How many variants have clinical significance annotations?"
- "Compare variant counts between samples"
Core Capabilities
| Capability | Description |
|---|---|
| VCF Parsing | Pure Python + cyvcf2 parsers. VCF 4.x, gzipped, multi-sample, SNV/indel/SV |
| Mutation Classification | Maps SO terms, SnpEff ANN, VEP CSQ, GATK Funcotator to standard types |
| VAF Extraction | Handles AF, AD, AO/RO, NR/NV, INFO AF formats |
| Filtering | VAF, depth, quality, PASS, variant type, mutation type, consequence, chromosome, SV size |
| Statistics | Ti/Tv ratio, per-sample VAF/depth stats, mutation type distribution, SV size distribution |
| Annotation | MyVariant.info (aggregates ClinVar, dbSNP, gnomAD, CADD, SIFT, PolyPhen) |
| SV/CNV Analysis | gnomAD SV population frequencies, DGVa/dbVar known SVs, ClinGen dosage sensitivity |
| Clinical Interpretation | ACMG/ClinGen CNV pathogenicity classification using haploinsufficiency/triplosensitivity scores |
| DataFrame | Convert to pandas for advanced analytics |
| Reporting | Markdown reports with tables and statistics, SV clinical reports |
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.
- 8d ago First seen · 449 lines · 238 tokens per session scan A 5e442a8197f5
tooluniverse-variant-analysis is a skill published in the GitHub repository AndyZhuang/Opentest (22 stars, last pushed 6mo ago), licensed MIT. It adds 238 tokens to every session and 4,144 once invoked, about $0.0012 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 2026-09-03.
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