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Annotation tools

ANNOVAR

  • SHORT NAME: ANNOVAR
  • FULL NAME: Annotate Variation
  • DESCRIPTION: ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).
  • URL : https://annovar.openbioinformatics.org/en/latest/
  • CITATION: Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data Nucleic Acids Research, 38:e164, 2010

VEP

  • SHORT NAME: VEP
  • FULL NAME: Ensembl Variant Effect Predictor
  • DESCRIPTION: The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.
  • URL : https://asia.ensembl.org/info/docs/tools/vep/index.html
  • CITATION: McLaren, W., Gil, L., Hunt, S.E. et al. The Ensembl Variant Effect Predictor. Genome Biol 17, 122 (2016). https://doi.org/10.1186/s13059-016-0974-4

loftee

  • SHORT NAME: LOFTEE
  • FULL NAME: Loss-Of-Function Transcript Effect Estimator
  • DESCRIPTION: A VEP plugin to identify LoF (loss-of-function) variation. Currently assesses variants that are:
  • Stop-gained
  • Splice site disrupting
  • Frameshift variants
  • URL : https://github.com/konradjk/loftee
  • CITATION: Karczewski, K.J., Francioli, L.C., Tiao, G. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020). https://doi.org/10.1038/s41586-020-2308-7

SnpEff

  • SHORT NAME: SnpEff
  • FULL NAME: SNP effect
  • DESCRIPTION: Genetic variant annotation and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
  • URL:http://pcingola.github.io/SnpEff/
  • CITATION: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672