bio-copy-number-cnvkit-analysis SKILL.md skillA
bio-copy-number-cnvkit-analysis from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-copy-number-cnvkit-analysis@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-copy-number-cnvkit-analysis/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 16,496 bytes
- Repository stars
- 662
- License
- MIT
Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility
Reference examples tested with: CNVkit 0.9.10+, samtools 1.19+, bedtools 2.31+, Python 3.10+, R 4.3+ with DNAcopy 1.76+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI: `cnvkit.py version` then `cnvkit.py batch --help` to confirm flags
- Python: `pip show cnvkit` then `python3 -c "import cnvlib; help(cnvlib.read)"`
- R: `packageVersion('DNAcopy')` (CBS backend)
If a command throws an unrecognized-argument or AttributeError, introspect the installed version and adapt the example rather than retrying. CNVkit segmentation methods (`hmm`, `hmm-tumor`, `hmm-germline`) depend on `pomegranate`; CBS depends on Bioconductor `DNAcopy`.
# CNVkit Copy Number Analysis
**"Detect copy number variants from my exome / panel data"** -> Run a read-depth pipeline: normalize on-target and off-target coverage against a reference, segment the log2-ratio profile, and call gains/losses. CNVkit is a *depth-only* caller — it estimates **relative** copy number and cannot, on its own, resolve tumor purity, ploidy, or allele-specific state. Choosing CNVkit is a decision that the experiment does not require allelic resolution.
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-copy-number-cnvkit-analysis@sha256:cbbc2e664bf95e05The line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_kmgvp6dhqhajftf4)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_kmgvp6dhqhajftf4 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-copy-number-cnvkit-analysis GET https://markdownregistry.com/api/v1/blob/cbbc2e664bf95e050fa597eb3fc74be18379cc9770fef535093fc82b08a432a8
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