BEAR Applications

snpEff 5.0e-GCCcore-11.2.0-Java-11

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

Accessing snpEff 5.0e-GCCcore-11.2.0-Java-11

To load the module for snpEff 5.0e-GCCcore-11.2.0-Java-11 please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load bear-apps/2022a
module load snpEff/5.0e-GCCcore-11.2.0-Java-11

BEAR Apps Version

2022a

Running snpEff

snpEff provides a wrapper script to avoid needing to call it via Java. To run snpeff you must get a copy of the config file and place it into your work directory cp $EBROOTSNPEFF/snpEff.config ./ You must then modify data.dir to be your working directory.

snpEff Databases

Searching for snpEff databases snpeff databases | grep ??? where ??? is the desired database if present you can download it using: snpEff download -v ??? -c snpEff.config If the database could not be found you would have to use the -dataDir flag and the location to this other database. Note: You must always inclue your modified config file in all snpEff actions.

More Information

For more information visit the snpEff website.

Dependencies

This version of snpEff has a direct dependency on: GCCcore/11.2.0 Java/11 Perl/5.34.0-GCCcore-11.2.0 Python/3.9.6-GCCcore-11.2.0

Other Versions

These versions of snpEff are available on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 14th February 2023