SnpEff

SnpEff is an open source tool that performs annotation on genetic variants and predicts their effects on genes by using an interval forest approach. This program takes pre-determined variants listed in a data file that contains the nucleotide change and its position and predicts if the variants are deleterious. This program was first developed to predict effects of single nucleotide polymorphisms (SNPs) in Drosophila. As of July 2024, this SnpEff paper has been cited 10076 times. SnpEff has been used for various applications – from personalized medicine, to profiling bacteria. This annotation and prediction software can be compared to ANNOVAR and Variant Effect Predictor, but each use different nomenclatures.