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

SnpSift is a toolbox that allows you to filter and manipulate annotated files.

• Version: 5.1
• Added: July, 2015
• Updated: June, 2023
• Link: https://pcingola.github.io/SnpEff/

See which versions of are available:

$ module avail snpeff

Load one into your environment and run it:

$ module load snpeff/5.1
$ snpeff

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip
$ sudo mkdir -p /export/apps/snpeff/5.1
$ sudo cp -r snpEff/* /export/apps/snpeff/5.1