usmanskillsmd variant-annotation
Query and annotate gene variants from ClinVar and dbSNP databases. Trigger when:
- User provides a variant identifier (rsID, HGVS notation, genomic coordinates) and asks about clinical significance
Variant Annotation
Query and annotate gene variants from ClinVar and dbSNP databases. Trigger when:
- User provides a variant identifier (rsID, HGVS notation, genomic coordinates) and asks about clinical significance
Overview
Variant Annotation is a comprehensive agent skill designed for tools workflows. It provides structured guidance and automation patterns that enable AI coding agents to handle variant annotation tasks with precision and reliability across diverse project environments.
This skill encapsulates best practices gathered from production deployments and open-source communities. It covers the complete lifecycle from initial setup through advanced configuration, ensuring consistent results whether you are working on a greenfield project or integrating into an existing codebase.
Built by openclaw, this skill follows the open SKILL.md standard and is compatible with all major AI coding tools including Claude Code, Cursor, Windsurf, Codex CLI, and ChatGPT.
When to Use
Activate this skill when the user needs to:
Set up or configure variant annotation in a new or existing project
Debug issues related to variant annotation implementation
Follow best practices for tools workflows
Automate repetitive variant annotation tasks
Review and improve existing variant annotation configurations
Integrate variant annotation with CI/CD pipelines or other tools
Core Capabilities
Automated Setup & Configuration
Generates complete configuration files with sensible defaults, proper directory structure, and environment-specific overrides. Includes inline documentation explaining each configuration choice and its tradeoffs.
Intelligent Code Generation
Produces idiomatic, production-ready code following established patterns and conventions. The generated code includes proper error handling, logging, type annotations, and test scaffolding out of the box.
Debugging & Troubleshooting
Systematically diagnoses common issues by analyzing error messages, log output, and configuration state. Provides step-by-step resolution guides with explanations of root causes to prevent recurrence.
Performance Optimization
Identifies bottlenecks and applies targeted optimizations based on measured data rather than assumptions. Tracks before/after metrics and documents the rationale behind each optimization decision.
Example Prompts
Users might ask:
"Set up variant annotation for my project"
"Debug why variant annotation is failing in CI"
"Optimize the variant annotation configuration for production"
"Add variant annotation support to the existing codebase"
"Review my variant annotation setup and suggest improvements"
"Migrate from the old variant annotation approach to the latest version"
Configuration
ParameterDefaultDescription
modeautoCLI mode: interactive, batch, or daemon
output_dir./outputDirectory for generated files and artifacts
verbosefalseEnable detailed logging for debugging
stricttrueEnforce strict validation on all inputs
timeout30000Maximum execution time in milliseconds
retry_count3Number of retry attempts on transient failures
Best Practices
Start with defaults — The default configuration is optimized for the most common use cases. Override only what you need to change.
Version control everything — Keep all configuration files and generated artifacts in version control for auditability and rollback capability.
Test in isolation first — Validate changes in a sandboxed environment before applying them to shared or production systems.
Document deviations — When you override defaults or apply custom configurations, document the reason in comments or a decisions log.
Monitor after changes — After applying any configuration change, monitor system behavior for at least one full cycle to catch unexpected regressions.
Keep dependencies updated — Regularly update dependencies and check for deprecation notices to avoid security vulnerabilities and compatibility issues.
Common Patterns
Quick setup
npx skills add openclaw/variant-annotation
Verify installation
skills verify variant-annotation
Run with custom config
skills run variant-annotation --mode=auto --verbose
Troubleshooting
IssueCauseSolution
Skill not foundPackage not installed or path incorrectRun npx skills add openclaw/variant-annotation to reinstall
Configuration errorInvalid parameter values or missing required fieldsRun skills validate variant-annotation to check config
Timeout exceededOperation taking longer than configured limitIncrease timeout parameter or optimize the operation
Permission deniedInsufficient access to target files or directoriesCheck file permissions and ensure write access to output directory
Integration Guide
Follow these steps to integrate Variant Annotation into your workflow:
Install the skill using your preferred package manager (npx, bunx, or pnpm)
Initialize configuration by running the setup wizard or copying the default config
Customize settings based on your project requirements and team conventions
Add to CI/CD by including the skill invocation in your pipeline configuration
Set up monitoring to track skill execution results and catch failures early
Output Format
This skill produces structured output in the following format:
{ "status": "success", "skill": "variant-annotation", "version": "1.0.0", "results": { "files_generated": 3, "warnings": [], "metrics": { "duration_ms": 1250, "memory_mb": 45.2 } } }
Advanced Usage
For power users and complex scenarios:
Chaining skills — Combine this skill with related skills for end-to-end workflows using the skills chain command
Custom templates — Override default templates by placing custom files in the .skills/templates/ directory
Environment variables — Configure behavior via environment variables prefixed with SKILL_ for container-friendly deployments
Hooks — Register pre/post execution hooks to run custom logic before or after the skill executes
Dry run mode — Use --dry-run flag to preview changes without applying them
Related Skills
Skills that work well alongside Variant Annotation:
Browse more skills in the Tools category
Check the full category listing for complementary tools