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

The following versions of SnpEff are available on OSC clusters:

Version Oakley owens
4.2 X* 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 without restriction.

Usage on Oakley

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}

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} , orjava -jar $SNPSIFT {other options}

Further Reading

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