variant-annotation - VCF variant annotation and prioritization tool
Annotates VCF variants using Ensembl VEP REST, ClinVar, and gnomAD data to produce prioritized summary reports.
Tags
Updated: 2026-09-23Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Parse standard VCF files
- Annotate variants with Ensembl VEP
- Extract ClinVar and population frequencies
- Prioritize variants by clinical severity
- Generate structured reports and tables
Inputs
- Input VCF or VCF.GZ file
Outputs
- Markdown annotation summary report
- JSON summary metrics and results
- TSV annotated variants table
- Reproducibility metadata directory
Requirements
- Python 3.10+
- pysam package
- requests package
- Ensembl VEP REST API access
- Linux or macOS operating system