SnpEff

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

Versions

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.

Access

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

Publisher/Vendor/Repository and License Type

http://snpeff.sourceforge.net, Open source

Usage 

Usage on Owens

Set-up

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.

Usage

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

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