VEP Web Tool

The VEP Web Tool provides automated annotation and predicted consequences for genomic variants described in VCFs or variant lists. It supports batch analysis and returns per-variant data including gene, transcript, the predicted consequence, amino acid changes, and HGVS notation. The tool is intended for researchers, clinicians, and bioinformaticians who need rapid annotation without local software installation.

Conceptually, input variants are aligned to reference transcripts for the selected organism and assembly. The tool computes consequences per transcript using standardized ranking (high/moderate/low/modifier) and can report all transcripts or a user-chosen primary transcript. Outputs are structured for programmatic ingestion and downstream pipelines.

Unique value includes real-time processing in a web environment, scalable handling of large variant sets, and optional integration with extra annotation sources. It reduces manual curation time, supports reproducible analysis, and fits both exploratory research and routine QC in clinical genomics.

Core features include: input in VCF or tab-delimited format; organism/assembly specification; transcript preference; per-variant annotations with gene, transcript, consequence, amino acid change, and HGVS; export options to TSV or JSON; and input/output ready for automated workflows. Typical use cases span variant discovery, annotation pipelines, and diagnostics research.