What is snpEff?

It's 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.

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Version: 2.1b (2012-04-26).

• Note If you are using hg19, it is recommended to download the latest database (due to improved RefSeq parsing in 2.1b).
• Added multi-threaded support (command line option '-t').
• GenBank support for building databases. See details here .
• Config file siplified
• E.Coli database added
• Galaxy download database option added.
• Added all ENSEMBL version 66 genomes
• Database 'download' issue solved. Apparently SourceForge servers were choking on URL that had double slashes, this should not happen. Implemented a workarround.
• SnpSift GWAS catalog: Annotate using GWAS Cataloga.
• SnpSift: Added 'varType' to annotate variant type (SNP/MNP/INS/DEL), as well as HOM/HET if possible.
• Faster VCF processing.
• Revision "2.1a" : Multi-thred race condition solved.
• Revision "2.1b" : Improved RefSeq parsing

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Related software

Some spinoffs from this project:

• MoreBs: A bisulphite sequencing analysis pipeline.
• SnpSift: A set of tools for filtering and selecting variants. Includes "SnpSift filter", which allows you to use arbitrary expressions to filter VCF files.

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Use example: 1000 Genomes SNP predictions

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

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Who is using SnpEff?

SnpEff is also being used by the following institutions (this is short and incomplete list):

• Broad Institute (MIT & Harvard)
• NIH (US)
• Harvard University
• Princeton University
• BGI (China)
• Massachusetts General Hospital
• Whitehead Institute, MIT
• Wellcome Trust Centre for Human Genetics (Oxford University)
• UC Berkeley
• Illumina
• Cambridge University (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)
• Bayer
• University of Cambridge (UK)
• Novartis
• Yale University
• Columbia University
• Stanford University
• Brown University
• Kyoto University (Japan)
• Genome Quebec (Canada)
• 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)
• Novocraft
• 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
• AstraZeneca
• Accelrys
• Johnson & Johnson
• Institute of Cancer Research (ICR), UK
• University of British Columbia (Canada)
• University of Southern California (USC)
• Arizona State University (ASU)
• Sanofi (France)

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Screen Snapshot

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