clinical-variant-reporter
CommunityGuideline-grade variant classification with evidence audit trails
Software Engineering#ACMG#variant classification#clinical genomics#pathogenicity#germline#secondary findings
AuthorMubasherMohammed
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill provides automated, guideline-grade classification of germline variants from VCF/BCF files, offering accurate, evidence-based ACMG classifications and generating detailed clinical interpretation reports.
Core Features & Use Cases
- ACMG/AMP 28-Criteria Evaluation: Assess each variant against a comprehensive evidence framework for ACMG classifications.
- Clinical Grade Reports: Generate reports with per-variant evidence audit trails and ACMG SF v3.2 secondary findings screening.
- Use Case: A geneticist can use this Skill to classify variants in a patient's VCF file, quickly identifying pathogenic or benign mutations, and generate a report with supporting evidence.
Quick Start
Use the clinical-variant-reporter skill to classify variants from the patient's VCF file and generate a report at the path '/output/report'.
Dependency Matrix
Required Modules
pysamrequestspandasmatplotlib
Components
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: clinical-variant-reporter Download link: https://github.com/MubasherMohammed/opencode-BioInfo/archive/main.zip#clinical-variant-reporter Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
Agent Skills Search Helper
Install a tiny helper to your Agent, search and equip skill from 620,000+ vetted skills library on demand.