SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

Availability and Restrictions


The following versions of SnpEff are available on OSC clusters:

Version Owens
4.2 X*
* Current default version

You can use  module spider snpeff to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


SnpEff is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type, Open source


Usage on Owens


To configure your environment for use of SnpEff, run the following command: module load snpeff. The default version will be loaded. To select a particular SnpEff version, use module load snpeff/version. For example, use module load snpeff/4.2 to load SnpEff 4.2.


This software consists of Java executable .jar files; thus, it is not possible to add to the PATH environment variable.

From module load snpeff, new environment variables, SNPEFF and SNPSIFT, will be set. Thus, users can use the software by running the following command: java -jar $SNPEFF {other options}, or java -jar $SNPSIFT {other options}.

Further Reading

Fields of Science: