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, BEARCloud VMs, and CaStLeS VMs):
module load snpEff/5.0e-GCCcore-11.2.0-Java-11
BEAR Apps Version
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.
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.
For more information visit the snpEff website.
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
These versions of snpEff are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.
|Version||BEAR Apps Version|
Last modified on 14th February 2023