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 subclonal-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/subclonal-copy-number)<a href="https://agentmods.dev/skills/gptomics/bioskills/subclonal-copy-number"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/subclonal-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/subclonal-copy-number"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/subclonal-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 | $0.00144 | $0.03473 |
| Opus 5 | $0.00072 | $0.01736 |
| Sonnet 5 | $0.00029 | $0.00695 |
| Haiku 4.5 | $0.00014 | $0.00347 |
Grade A, and why
bio-copy-number-subclonal-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 7d 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-subclonal-copy-number — 98% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 212 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: R 4.3+ with Battenberg 2.2.10+ and TitanCNA 1.40+, MEDICC2 1.0+, Python 3.10+; impute2/Beagle phasing reference panels.
Before using code patterns, verify installed versions match. If versions differ:
- R:
packageVersion('Battenberg')/'TitanCNA')then?function - CLI:
medicc2 --help - Battenberg is GitHub-only (
Wedge-lab/battenberg) and needs a 1000 Genomes impute/phasing reference and allele-counter; confirm reference data is installed
Battenberg and TITAN both consume allele-specific data (logR + BAF at heterozygous SNPs); they cannot run on relative copy ratio alone.
Subclonal Copy Number and Tumor Evolution
"This copy number is non-integer — is it noise, or are there subclones" -> A tumor is a mixture of cell populations. When a copy-number change is present in only some cancer cells, bulk sequencing averages it into a non-integer state. A long non-integer segment is not noise — it is a subclonal copy-number alteration, and resolving it reveals the tumor's clonal architecture.
- R:
Battenberg(phased clonal + subclonal CN),TitanCNA(HMM mixture of cell populations) - CLI:
medicc2(whole-genome-doubling-aware copy-number phylogenies) - Input: allele-specific data — see allele-specific-copy-number for the clonal layer
Clonal vs Subclonal — What the Tools Output
| Concept | Meaning |
|---|---|
| Clonal CNA | Present in all cancer cells; one copy-number state per segment |
| Subclonal CNA | Present in a fraction of cancer cells; the segment needs two states plus a fraction |
| Cancer cell fraction (CCF) | Fraction of cancer cells carrying the event |
| Mirrored subclonal allelic imbalance | Different subclones lose opposite haplotypes of the same region |
Battenberg fits a clonal allele-specific profile (ASCAT internally), then where a segment fits poorly as a single integer state, it models it as a mixture of two states with a subclonal fraction. TITAN uses an HMM whose states span multiple clonal clusters, jointly estimating per-cluster cellular prevalence. Both need haplotype phasing — subclonal allelic imbalance is only resolvable when SNPs are phased.
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.
- 7d ago First seen · 212 lines · 144 tokens per session scan A 07881011331d
bio-copy-number-subclonal-copy-number is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 144 tokens to every session and 3,473 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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