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 GPTomics/bioSkills --skill cnv-annotationgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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/gptomics/bioskills/cnv-annotation)<a href="https://agentmods.dev/skills/gptomics/bioskills/cnv-annotation"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/cnv-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/gptomics/bioskills/cnv-annotation"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/cnv-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 | $0.00132 | $0.03361 |
| Opus 5 | $0.00066 | $0.01681 |
| Sonnet 5 | $0.00026 | $0.00672 |
| Haiku 4.5 | $0.00013 | $0.00336 |
Grade A, and why
bio-copy-number-cnv-annotation 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.
Copies of this mod
1 near-identical copy found in the catalogue:
- bio-copy-number-cnv-annotation — 100% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 224 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: bedtools 2.31+, AnnotSV 3.4+, Python 3.10+ with pybedtools 0.9+, pandas 2.2+, pysam 0.22+; R 4.3+ with clusterProfiler 4.10+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
bedtools --version,AnnotSV --version - Python:
pip show pybedtools pandas pysam - R:
packageVersion('clusterProfiler')
If code throws an error, introspect the installed package and adapt the example. AnnotSV output column names change between major versions — verify against the installed version.
CNV Annotation
"Annotate my CNV calls with the genes they affect" -> Overlap CNV segments with gene models, dosage-sensitivity maps, and clinical databases. The hard part is not the intersection — it is deciding which genes matter. A focal amplification overlapping 30 genes usually has one driver (the peak gene); a deletion's consequence depends on whether each gene is dosage-sensitive and whether the whole gene or only part is removed.
- CLI:
bedtools intersect -a cnvs.bed -b genes.bed -wa -wb;AnnotSVfor full annotation - Python:
pybedtoolsfor interval logic;pysamfor VCF database queries
Annotation Strategy — Pick the Database for the Question
| Question | Resource | What it answers |
|---|---|---|
| Which genes does this CNV span? | RefSeq/GENCODE gene BED | Raw overlap (not yet consequence) |
| Is loss of this gene damaging? | ClinGen haploinsufficiency (HI) score | Dosage sensitivity to deletion |
| Is gain of this gene damaging? | ClinGen triplosensitivity (TS) score | Dosage sensitivity to duplication |
| Is this CNV common in the population? | gnomAD-SV, DGV, 1000G CNV | Benign-frequency filtering |
| Is this a known recurrent disorder locus? | ClinGen dosage regions, DECIPHER | Genomic-disorder context |
| Is this a cancer driver? | COSMIC Cancer Gene Census, OncoKB | Oncogene vs tumor-suppressor role |
| Is there pathogenic small-variant content? | ClinVar | Coincident SNV/indel pathogenicity |
| One-shot comprehensive annotation + ranking | AnnotSV | Aggregates most of the above |
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.
- 8d ago First seen · 224 lines · 132 tokens per session scan A fef68270f317
bio-copy-number-cnv-annotation is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 27d ago), licensed MIT. It adds 132 tokens to every session and 3,361 once invoked, about $0.0007 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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