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SnpEff

Annotates and predicts the effects of single nucleotide polymorphisms (SNPs). SnpEff features include: (1) the ability to make thousands of predictions per second; (2) the ability to add custom genomes and annotations; (3) the ability to integrate with Galaxy (4) compatibility with multiple species and multiple codon usage tables, (5) integration with Broad's Genome Analysis Toolkit (GATK) and (6) the ability to perform non-coding annotations. It enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.

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1 user review

1 user review

Arup Ghosh's avatar image Arup Ghosh's country flag

Arup Ghosh

Really easy to use variant annotation tools compatible with multiple variant calling software outputs. This tool gives the freedom to build custom annotation files and direct import from NCBI GeneBank.

SnpEff forum

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SnpEff classification

  • Animals
    • Homo sapiens

SnpEff specifications

Interface:
Web user interface
Input data:
Predicted variants (SNPs, insertions, deletions, MNPs)
Output data:
SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes).
Stability:
Stable
Restrictions to use:
None
Input format:
VCF
Computer skills:
Basic
Maintained:
Yes

Subtools

  • SnpSift
  • ClinEff

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No review has been posted.

SnpEff forum

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No open topic.

SnpEff classification

  • Animals
    • Homo sapiens

SnpEff specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
VCF
Operating system:
Unix/Linux
License:
GNU Lesser General Public License version 3.0
Version:
4.3
Source code URL:
http://snpeff.sourceforge.net/download.html#source
Interface:
Command line interface
Input data:
Predicted variants (SNPs, insertions, deletions, MNPs)
Output data:
SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes).
Programming languages:
Java
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

Subtools

  • SnpSift
  • ClinEff

SnpEff distribution

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SnpEff support

Documentation

Maintainer

  • Douglas M. Ruden <>
  • Douglas M. Ruden <>

Additional information

http://www.dnaminer.com/clineff.html

Credits

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Publications

Institution(s)

Supported by a Michigan Core Technology grant from the State of Michigan's 21st Century Fund Program to the Wayne State University Applied Genomics Technology Center, the Environmental Health Sciences Center in Molecular and Cellular Toxicology with Human Applications Grant P30 ES06639 at Wayne State University, NIH R01 grants (ES012933) and DK071073.

Link to literature

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