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 zamushwani/biomedical-ai-skills --skill variant-annotationgit clone --depth 1 https://github.com/zamushwani/biomedical-ai-skillsWrote 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/zamushwani/biomedical-ai-skills/variant-annotation)<a href="https://agentmods.dev/skills/zamushwani/biomedical-ai-skills/variant-annotation"><img src="https://agentmods.dev/badge/skills/zamushwani/biomedical-ai-skills/variant-annotation/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/zamushwani/biomedical-ai-skills/variant-annotation"><img src="https://agentmods.dev/badge/skills/zamushwani/biomedical-ai-skills/variant-annotation.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 | $0.00000 | $0.05683 |
| Opus 5 | $0.00000 | $0.02841 |
| Sonnet 5 | $0.00000 | $0.01137 |
| Haiku 4.5 | $0.00000 | $0.00568 |
Grade A, and why
variant-annotation scanned grade A with 1 finding 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 12d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
curl -H "Authorization: Bearer $ONCOKB_TOKEN" \ How it starts
The opening of the file, as written. The whole thing — 512 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Variant Annotation
Annotation and clinical interpretation of DNA variants in cancer. Covers VCF normalization and filtering, functional annotation with VEP, germline classification under ACMG/AMP, somatic classification under the AMP/ASCO/CAP tiers and the ClinGen/CGC/VICC oncogenicity standard, tumor mutational burden, microsatellite instability, and neoantigen prediction.
When to Use This Skill
Activate when the user requests:
- VCF filtering, normalization, or merging
- Functional annotation (VEP, SnpEff, ANNOVAR)
- Germline variant classification (ACMG/AMP, pathogenic vs benign)
- Somatic variant classification (tiers, oncogenicity, actionability)
- Driver vs passenger discrimination
- OncoKB or CIViC evidence lookup
- Tumor mutational burden calculation
- Microsatellite instability estimation
- Neoantigen prediction or HLA binding
- Interpreting a variant of uncertain significance
Inputs
| Data Type | Format | Source |
|---|---|---|
| Variant calls | VCF 4.2+, bgzipped and indexed | GATK, Mutect2, DeepVariant, Strelka2 |
| Reference genome | FASTA with .fai |
GRCh38 (or GRCh37 for legacy cohorts) |
| Somatic MAF | Mutation Annotation Format | TCGA GDC, cBioPortal |
| Panel definition | BED | Assay manufacturer, for TMB denominators |
| HLA type | 4-digit alleles | OptiType, HLA-HD, arcasHLA |
Environment
Versions verified 2026-08.
bcftools 1.24 VCF manipulation, normalization
Ensembl VEP 116.1 functional annotation, the current default
SnpEff 5.4c alternative annotator
ANNOVAR current still distributed, registration required
Bioconductor
VariantAnnotation 1.58.0 VCF parsing and coding consequences in R
maftools 2.28.0 somatic MAF summarization, TMB, signatures
Neoantigens
pVACtools 7.1.2 neoantigen pipeline (griffithlab)
NetMHCpan 4.1+ MHC class I binding; academic licence
Microsatellite instability, and which tool is still alive:
msisensor ARCHIVED. ding-lab/msisensor was archived, last push 2021.
Do not start new work on it.
msisensor-pro v1.3.0 (2024-09). Current choice, tumor-only or paired.
msisensor2 last push 2024-04. Tumor-only, no matched normal.
MANTIS paired tumor/normal, still used in clinical settings.
All four are read-based. MSI can also be inferred from a panel using
MSIsensor-pro's baseline mode, but the baseline must be built on the same
assay or the calls are not comparable.
What ships with it
6 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.
- 12d ago First seen · 512 lines · 0 tokens per session scan A 3859d1d29e72
variant-annotation is a skill published in the GitHub repository zamushwani/biomedical-ai-skills (1 stars, last pushed 13d ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 5,683 tokens. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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