SnpEff

Genetic variant annotation and effect prediction toolbox.

Download SnpEff
Latest version 3.5 (2014-03-11)
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 9,000 genomes.
  • Cancer variants analysis
  • GATK compatible (-o gatk)
  • HGSV notations support (clinical)

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Version 3.5

Several improvement and bug fixes.

  • Improvements in Sequence Ontology
  • SnpSift dbNSFP: Tabix indexed files
  • Galaxy support: Improvements and bug fixes
  • Project source moved to GitHub
  • Bug fixes: Indels
  • Support for large chromosomal deletions

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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

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

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