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 allele-specific-copy-numbergit 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/allele-specific-copy-number)<a href="https://agentmods.dev/skills/gptomics/bioskills/allele-specific-copy-number"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/allele-specific-copy-number/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/allele-specific-copy-number"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/allele-specific-copy-number.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 | $0.00176 | $0.04325 |
| Opus 5 | $0.00088 | $0.02162 |
| Sonnet 5 | $0.00035 | $0.00865 |
| Haiku 4.5 | $0.00018 | $0.00432 |
Grade A, and why
bio-copy-number-allele-specific-copy-number 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-allele-specific-copy-number — 95% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 241 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: ASCAT 3.1+, Sequenza 3.0+ (sequenza-utils 3.0+), FACETS 0.6+ (snp-pileup), PureCN 2.6+, R 4.3+, Python 3.10+.
Before using code patterns, verify installed versions match. If versions differ:
- R:
packageVersion('ASCAT')/'sequenza'/'facets'/'PureCN', then?function - CLI:
sequenza-utils --version,snp-pileup --help
Sequenza 3.0 depends on the copynumber Bioconductor package, REMOVED from Bioconductor 3.18+ (2023). Install a maintained fork (ShixiangWang/copynumber or igordot/copynumber) before Sequenza will load. ASCAT's GC-correction function was renamed across 2.x->3.x (ascat.GCcorrect -> ascat.correctLogR) — verify against the installed version.
Allele-Specific Copy Number
"How many copies of each allele, in what fraction of cells, at what tumor purity" -> Jointly model read depth and B-allele frequency to fit tumor purity, ploidy, and integer major/minor copy number per segment. Depth alone gives only relative copy ratio; depth + BAF gives absolute allele-specific copy number. This skill is required whenever the question involves LOH, absolute copy number, purity, ploidy, or whole-genome doubling — CNVkit and GATK somatic CNV cannot answer those.
- R:
ASCAT(WGS, SNP array),sequenza(WES/WGS),facets(panel/WES/WGS),PureCN(tumor-only panel/WES) - CLI:
purple(Hartwig WGS pipeline, with AMBER + COBALT)
The Identifiability Problem — Why This Is Hard
Purity and ploidy are not identifiable from depth alone. The same log-ratio profile is explained equally well by many (purity, ploidy) pairs: a homozygous deletion at 30% purity looks identical to a heterozygous deletion at 60% purity; an entire profile can be reinterpreted at 2x ploidy with halved purity. Every allele-specific caller breaks this degeneracy by adding BAF — allelic imbalance constrains which solution is real. The consequence: the likelihood surface is multimodal, the fit can lock onto an integer-multiple of the true ploidy, and a single point estimate must never be trusted without inspecting the fit diagnostic (ASCAT sunrise plot, Sequenza cellularity/ploidy contour, FACETS dipLogR). A documented example: the same tumor scored ploidy 4.27 by FACETS (WGS) and 2.42 by ASCAT (SNP array).
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 · 241 lines · 176 tokens per session scan A ee43e209b5e8
bio-copy-number-allele-specific-copy-number is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 27d ago), licensed MIT. It adds 176 tokens to every session and 4,325 once invoked, about $0.0009 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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