SnpEff

Genetic variant annotation and effect prediction toolbox.

Download SnpEff
Important: This version implements the new VCF annotation standard 'ANN' field.
Latest version 4.3g (2016-11-28)
Requires Java 1.7

ClinEff (new)

Professional verison of SnpEff & SnpSift suites. ClinEff is considered more stable thus suitable for Clinical and Production operations, whereas SnpEff/SnpSfit is designed for Research and Academic usage.
Features:

  • Compliance support (CLIA and CAP)
  • Long Term Support
  • Prioritized bug fixes and feature development
  • Customized databases and annotation pipelines
  • Integration with open, private and proprietary databases
  • Privacy: Tickets, issues, pipeline-specific analysis

View details »

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 38,000 genomes.
  • Standard ANN annotation format
  • Cancer variants analysis
  • GATK compatible (-o gatk)
  • HGVS notation
  • Sequence Ontology standardized terms

View details »

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

View details »

Version 4.3

Features:

  • Significant improvements in translocations annotations
  • Improvements in large structural variant annotaions
  • Protein-Protein interaction loci annotations (from PDB)

View details »

Paper & Citing

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

View details »

Who uses SnpEff?

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

View details »

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.

View details »