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, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2021b
module load snpEff/5.0e-GCCcore-11.2.0-Java-11

BEAR Apps Version

2021b

Architectures

EL8-cascadelake — EL8-haswell — EL8-icelake — Ubuntu20.04-haswell

The listed architectures consist of two part: OS-CPU.

• BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
• BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

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, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 14th February 2023