SnpEff

Description and basic information.

SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

Typical usage :

  • Input: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF).

  • Output: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes). A list of effects and annotations that SnpEff can calculate can be found here.

If you are using SnpEff or SnpSift, please cite our work.

  • Citing SnpEff (you can find the paper here):
    "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 [PubMed - in process]

    BibTex entry:

    @article{cingolani2012program,
      title={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},
      author={Cingolani, P. and Platts, A. and Coon, M. and Nguyen, T. and Wang, L. and Land, S.J. and Lu, X. and Ruden, D.M.},
      journal={Fly},
      volume={6},
      number={2},
      pages={80-92},
      year={2012}
    }
    

  • Citing SnpSift (you can find the paper here):
    "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
    BibTex entry:
    @article{cingolani2012using,
      title={Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift},
      author={Cingolani, P. and Patel, V.M. and Coon, M. and Nguyen, T. and Land, S.J. and Ruden, D.M. and Lu, X.},
      journal={Frontiers in Genetics},
      volume={3},
      year={2012},
      publisher={Frontiers Media SA}
    }
    

SnpEff is really fast, it can calculate predictions for all the SNPs in the 1000 Genomes project in less than 15 minutes. A summary page can be found here. Effect predictions in VCF and TXT formats.

SnpEff is open source. It is released as "LGPLv3".

Users of SnpEff include most major research and academic institutions, as well as pharmaceutical companies and clinical sequencing projects.

Some Academic & Research institutions using SnpEff:

  • Broad Institute (MIT & Harvard)
  • NIH (US)
  • Harvard University
  • Princeton University
  • BGI (China)
  • Massachusetts General Hospital
  • Whitehead Institute, MIT
  • Wellcome Trust Sanger Institute (UK)
  • UC Berkeley
  • Wellcome Trust Centre for Human Genetics (UK)
  • University of Cambridge (UK)
  • Duke University
  • Max Planck (Germany)
  • Cold Spring Harbor Laboratory (CSHL)
  • Institut Pasteur (France)
  • NCI / NIH (National Cancer Institute, US)
  • McGill University (Canada)
  • EMBL (Cambridge, UK)
  • University of Toronto (Canada)
  • University of Cambridge (UK)
  • Yale University
  • Columbia University
  • Stanford University
  • Brown University
  • Genome Quebec (Canada)
  • Centre national de la recherche scientifique (CNRS, France)
  • University of Michigan
  • Kyoto University (Japan)
  • Institut National de la Recherche Agronomique (INRA, France)
  • University of Wisconsin-Madison
  • UT Southwestern Medical Center
  • University of Southern California
  • Bologna University (Italy)
  • Casa Sollievo della Sofferenza - Mendel (Italy)
  • Universitat Wien (Vienna, Austria)
  • Ottawa University (Canada)
  • Peter MacCallum Cancer Centre (Australia)
  • University of Alabama Birmigham
  • University of Bristol (UK)
  • UC-Davis (California)
  • Winsconsin University
  • TUM University (Germany)
  • The Translational Genomics Institute (Tgen)
  • Rutgers University (New Jersey)
  • Nagasaki University (Japan)
  • Washington University
  • Netherlands Cancer Institute (NKI)
  • Centro Nacional de Biotecnología, (National Center for Biotecnology) CNB-CSIC, Madrid, Spain
  • University of California-Riverside
  • Carleton University (Canada)
  • Memorial Sloan-Kettering Cancer Center
  • Boston University
  • University of California, San Francisco (UCSF)
  • Institute of Cancer Research (ICR), UK
  • University of Virginia
  • University of British Columbia (Canada)
  • Seoul National University (Korea)
  • University of Southern California (USC)
  • Arizona State University (ASU)
  • NeuroTexas Institute at St. David's HealthCare
  • University of Otago (New Zealand)
  • Queensland Institute of Medical Research (Australia)
  • National University of Singapore (NUS)
  • Children's Hospital of Philadelphia
  • Technion (Israel)
  • Queensland UNiversity (Australia)
  • Vall d'Hebron Research Institute: VHIR (Barcelona. Catalonia. Spain)
  • University of Pretoria (South Africa).
  • Centrum Wiskunde & Informatica (Amsterdam, Netherlands)
  • Technical University of Denmark: DTU (Denmark)
  • Spanish National Research Council (CSIC, Spain)
  • Swedish University of Agricultural Sciences: SLU (Sweden)
  • University of Iowa
  • Bilkent University (Turkey)
  • The Hebrew University of Jerusalem (Israel)
  • Laboratory of Malaria and Vector Research NIH/NIAID
  • Max F. Perutz Laboratories: MFPL (Vienna, Austria)
  • Animal Health Trust: AHT (UK)
  • BC Cancer Agency (Canada)
  • University of California, Irvine
  • University College London (London, UK)
  • Centro Nacional de AnĂ¡lisis GenĂ³mico: CNAG (Barcelona, Spain)
  • Advanced Genomics and Bioinformatic Research Center (Turkey)

Some private Companies & Corporations users of SnpEff:

  • Bayer
  • Novartis
  • Illumina
  • Johnson & Johnson
  • AstraZeneca
  • Novocraft
  • Sanofi (France)
  • Accelrys
  • DnaNexus
  • Bio-Prodict (Netherlands)
  • Spiral Genetics
  • Covance
  • Eisai (Japan)
  • EdgeBio
  • BioBase
  • Counsyl

Note: These are not by any means comprehensive lists.

SnpEff is integrated with other tools commonly used in sequencing data analysis pipelines. Most notably Galaxy, GATK and GKNO projects support SnpEff. By using standards, such as VCF, SnpEff makes it easy to integrate with other programs.

This is a screen capture from a Galaxy server (click to enlarge)