cnvkit-copy-number SKILL.md skillA
cnvkit-copy-number from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/cnvkit-copy-number@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/variant/cnvkit-copy-number/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 23,535 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
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.
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
# CNVkit Copy Number Analysis ## Overview CNVkit detects somatic copy number variants (CNVs) from whole-exome sequencing (WES), whole-genome sequencing (WGS), or targeted panel BAM files. It calculates read depth in both on-target (capture) bins and off-target (antitarget) bins, corrects for GC bias and library depth, segments the log2 copy ratio profile with circular binary segmentation (CBS) or a hidden Markov model (HMM), and calls amplifications and deletions. CNVkit provides both a CLI (`cnvkit.py`) and a Python API (`cnvlib`) for integration into analysis pipelines, and produces scatter plots, chromosome diagrams, heatmaps, and export files in VCF, BED, and SEG formats. ## When to Use - Calling somatic copy number variants from tumor-normal paired exome (WES) or targeted panel sequencing - Detecting copy number alterations in tumor-only samples using a pooled normal reference - Running CNV analysis on whole-genome sequencing (WGS) data with the `--method wgs` mode - Estimating tumor purity and ploidy for samples where purity is unknown, to interpret copy ratio calls - Generating SEG format copy number files for GISTIC2, cBioPortal, or IGV visualization …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/cnvkit-copy-number@sha256:d6b0c34985711ee6The line at the top of this page pins the label git:20260929.7a7d60f, 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_detthdwulyjhxodl)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 41 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 23,535 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 23,584 B | A | view · diff |
| git:20260827.cbbeb75 | 2026-08-27 | cbbeb75 | 21,544 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 22,168 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (23535 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_detthdwulyjhxodl GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/cnvkit-copy-number GET https://markdownregistry.com/api/v1/blob/d6b0c34985711ee6a0cb6c4014bc88b361ee89e63b87304199a97432c12b9746
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.