CNVkit (Claude Skill)

Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x).


Type	Claude Skill
Supplier	jaechang-hits (community OSS, CC BY 4.0)
Availability	GA — part of the BixBench-evaluated SciAgent-Skills collection
Pricing	Free / OSS (Apache-2.0)
Capabilities	Read/Write — Claude runs the skill’s Python locally (Bash), not as an MCP tool

How to install

SciAgent-Skills is not an npm package — skills are plain markdown read directly by the agent (no npx/npm).

Claude Code — clone and load as a plugin:
```
git clone https://github.com/jaechang-hits/SciAgent-Skills
```
Then inside Claude Code run /plugin install sciagent-skills (verify it appears under /plugin → Installed). Clone into your project directory so Claude Code picks the skills up via CLAUDE.md.
Manual / other agents — point the agent at the skill file directly:
```
cp -r SciAgent-Skills/skills/genomics-bioinformatics/variant/cnvkit-copy-number ~/.claude/skills/
```
The skill declares its own Python dependencies in its SKILL.md; install them when prompted on first use.

What it does

Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x). Bin coverage in target/antitarget regions, normalize vs reference, segment with CBS/HMM, call amps/dels, scatter/diagram plots, purity/ploidy, VCF/SEG export. CLI plus Python API (cnvlib). Use GATK CNV for deep WGS with population controls; use CNVkit for targeted/exome where antitarget bins matter.

Primary use cases: Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x).

Notes

Distributed as a SKILL.md (plus code examples) in the SciAgent-Skills collection — Claude executes it locally via Bash/Python rather than as an MCP server. Upstream license: Apache-2.0. The skill directory upstream is skills/genomics-bioinformatics/variant/cnvkit-copy-number.

Sources

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