VEP (Variant Effect Predictor)

Overview

VEP (Variant Effect Predictor), developed by Ensembl, annotates genetic variants with their predicted functional consequences (e.g., synonymous, missense, stop-gain, splice-site) using transcript databases and external tools (SIFT, PolyPhen-2, etc.). In the TCGA MC3 pipeline, VEP is invoked as part of the vcf2maf annotation step to assign functional consequence to each variant.

Used by

• Invoked as part of the vcf2maf annotation step in the TCGA MC3 pipeline for functional consequence annotation of ~22.5M somatic variants across 10,510 TCGA tumor/normal pairs PMID:29596782

Notes

• VEP is the standard annotation engine used by vcf2maf; the version used affects HGVS notation and consequence predictions.
• Annotation accuracy depends on the transcript build and version of VEP used; MC3 used vcf2maf v1.6.11.

Sources

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