SnpEff

Genetic variant annotation and effect prediction toolbox.

Download SnpEff
Latest version 4.0 E (2014-09-13)
Requires Java 1.7

SnpEff

Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).
Features:

  • Supports over 20,000 genomes.
  • Cancer variants analysis
  • GATK compatible (-o gatk)
  • HGVS notation
  • Sequence Ontology standardized terms

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Version 4.0

Major improvements and support for standards:

  • HGVS notations
  • Sequence Ontology terms
  • Easier to use
  • SnpEff downloads databases automatically
  • Automatic third party databases downloads
  • Support for GRCh38
  • Support for Ebola Zaire Virus (2014 West Africa outbreak)

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SnpSift

SnpSift helps filtering and manipulating genomic annotated files (VCF). Once you annotated your files using SnpEff, you can use SnpSift to help you filter large genomic datasets in order to find the most significant variants

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Paper & Citing

If you are using SnpEff or SnpSift in an research or academic environment, please cite our papers.

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Who uses SnpEff?

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

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Galaxy, GATK & GKNO

SnpEff is integrated with other tools commonly used in sequencing data analysis pipelines. Most notably Galaxy, GATK and GKNO projects support SnpEff.

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