bio-copy-number-gatk-cnv SKILL.md skillA
bio-copy-number-gatk-cnv 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-gatk-cnv@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-gatk-cnv/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 15,685 bytes
- Repository stars
- 662
- License
- MIT
Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK…
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: GATK 4.5+ (gatk4), Python 3.10+ (gcnv conda env), R 4.3+. Before using code patterns, verify installed versions match. If versions differ: - CLI: `gatk --version` then `gatk <ToolName> --help` to confirm arguments - gCNV requires a working `gatkcondaenv` (theano/tensorflow stack) — `gatk` will report if the Python environment is missing GATK 4.5+ gCNV inference defaults are tuned for whole-exome data; whole-genome runs generally need parameter changes. If a tool reports an unrecognized argument, check the help for that exact GATK version rather than retrying. # GATK CNV Workflows **"Call CNVs the GATK way"** -> GATK has two *separate* CNV workflows that share almost no tools. Picking the wrong one is the most common mistake. - Somatic CNV: `CollectReadCounts` -> `DenoiseReadCounts` -> `ModelSegments` -> `CallCopyRatioSegments`. Tumor copy-ratio segments, optionally allele-aware. - Germline gCNV: `DetermineGermlineContigPloidy` -> `GermlineCNVCaller` -> `PostprocessGermlineCNVCalls`. Per-sample germline CN genotypes (VCF). ## Critical: What GATK Somatic CNV Does NOT Provide …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-copy-number-gatk-cnv@sha256:e8aa132fae56c692The 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_2c6kr3t3nvoe77cp)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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- 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
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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_2c6kr3t3nvoe77cp GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-copy-number-gatk-cnv GET https://markdownregistry.com/api/v1/blob/e8aa132fae56c6920fba379cea9beb11e10ee32de0e5c9e7ea1c9fa04e608071
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.