bio-clinical-databases-variant-prioritization SKILL.md skillA
bio-clinical-databases-variant-prioritization 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-clinical-databases-variant-prioritization@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-clinical-databases-variant-prioritization/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 25,271 bytes
- Repository stars
- 662
- License
- MIT
Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP…
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: pandas 2.2+, cyvcf2 0.30+, pyhgvs 0.12+, Exomiser 14.0+ (Smedley 2015), Phen2Gene 1.2+ (Zhao 2020), DeNovoGear 1.1.1+ (Ramu 2013), WhatsHap 2.0+ (Patterson 2015), HPO 2024+ (Human Phenotype Ontology). ACMG Secondary Findings list is v3.2 (Miller 2023): 81 genes. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. Phenotype-driven prioritization REQUIRES high-quality HPO terms; without rich phenotypic input Exomiser/AMELIE degrade significantly. # Rare-Disease Variant Prioritization Pipeline **'Prioritize candidate disease-causing variants from this trio exome'** -> Filter to rare + functional + inheritance-consistent variants; rank by phenotype concordance; flag ACMG SF v3.2 incidental findings; report tiers with classification logic deferred to `acmg-classification`. …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-clinical-databases-variant-prioritization@sha256:031bf338ee4a7712The 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_pk57ewv3gletmidu)
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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 curl or wget piped into a shell
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- pass: No instruction to read or print local credentials
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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_pk57ewv3gletmidu GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-clinical-databases-variant-prioritization GET https://markdownregistry.com/api/v1/blob/031bf338ee4a771243f6ae4eed074858c099f97675b4ef4bc9df520205bac894
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.