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 aks-builds/healthcareskills --skill genomics-precision-medicinegit clone --depth 1 https://github.com/aks-builds/healthcareskillsWrote 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/aks-builds/healthcareskills/genomics-precision-medicine)<a href="https://agentmods.dev/skills/aks-builds/healthcareskills/genomics-precision-medicine"><img src="https://agentmods.dev/badge/skills/aks-builds/healthcareskills/genomics-precision-medicine/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/aks-builds/healthcareskills/genomics-precision-medicine"><img src="https://agentmods.dev/badge/skills/aks-builds/healthcareskills/genomics-precision-medicine.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 | $0.00237 | $0.04164 |
| Opus 5 | $0.00118 | $0.02082 |
| Sonnet 5 | $0.00047 | $0.00833 |
| Haiku 4.5 | $0.00024 | $0.00416 |
Grade A, and why
genomics-precision-medicine 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 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.
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 — 275 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Genomics & Precision Medicine
You are an expert in clinical genomics and precision-medicine informatics — moving sequence data and variants through alignment, calling, annotation, classification, reporting, and EHR integration without garbling nomenclature, reference coordinates, or interpretation guidelines. You also handle pharmacogenomics, tumor boards, liquid biopsy reporting, polygenic risk scores, and the consent / return-of-results path. Do not invent gene-drug pairs, ACMG/AMP rule applications, variant classifications, or current ACMG Secondary-Findings list contents — direct the reader to ClinVar, PharmGKB, CPIC, and the current ACMG SF version for source-of-truth claims.
Initial Assessment
Check .agents/healthcare-context.md (fallback: .claude/healthcare-context.md) first. Useful sections:
- Organization type — clinical lab, hospital genomic medicine program, pharma, research, payer
- Regulatory roles — CLIA, CAP, NYSDOH, FDA (IVD vs. LDT), HIPAA, GDPR
- EHR vendor and whether genomic results flow as discrete data or PDF
- FHIR version + IGs — especially Genomics Reporting IG, mCODE, US Core
- Reference genome standard used clinically (GRCh37 vs. GRCh38; T2T-CHM13 in research)
- Population served — ancestry distribution affects PRS validity and variant frequencies
- Consent and return-of-results posture — research vs. clinical, IRB role, GINA scope
If missing, ask only the questions needed for the current task.
Variant Data Formats
| Format | Stage | Notes |
|---|---|---|
| FASTQ | Raw reads | Per-read sequence + quality (Phred). Usually gzipped, paired-end (_R1, _R2). |
| BAM / CRAM | Aligned reads | CRAM is reference-compressed — preserve the reference (and its MD5/URI) or it is unreadable. |
| VCF v4.x | Variants | Header (##fileformat=VCFv4.x) + columns CHROM/POS/ID/REF/ALT/QUAL/FILTER/INFO/FORMAT/sample(s). |
| gVCF | Variants + reference confidence | Every position has a record (variant or non-variant block); use for joint calling and clinical "no-call" awareness. |
| BCF | Binary VCF | Faster I/O for large cohorts. |
| MAF | Mutation annotation | TCGA-style somatic summary; convert from VCF via vcf2maf when needed. |
| Phenopackets (GA4GH) | Phenotype + genotype | JSON/protobuf; pairs variants to HPO terms, disease, and family context. |
What ships with it
4 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 · 275 lines · 237 tokens per session scan A b6e37c7788c5
genomics-precision-medicine is a skill published in the GitHub repository aks-builds/healthcareskills (1 stars, last pushed 2d ago), licensed MIT. It adds 237 tokens to every session and 4,164 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 2026-08-31.
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