VEPerform: a web resource for evaluating the performance of variant effect predictors

TL;DR

VEPerform is a web tool that evaluates the performance of variant effect predictors at the gene level using balanced precision-recall analysis, aiding in more accurate classification of missense variants.

Contribution

It introduces VEPerform, a novel web-based platform for gene-level VEP performance evaluation using balanced precision-recall curves, addressing imbalanced test set challenges.

Findings

Provides a user-friendly web interface for VEP evaluation.

Utilizes balanced precision-recall curves for more accurate assessment.

Facilitates better classification of pathogenic variants.

Abstract

Computational variant effect predictors (VEPs) are providing increasingly strong evidence to classify the pathogenicity of missense variants. Precision vs. recall analysis is useful in evaluating VEP performance, especially when adjusted for imbalanced test sets. Here, we describe VEPerform, a web-based tool for evaluating the performance of VEPs at the gene level using balanced precision vs. recall curve (BPRC) analysis.