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: 4.1g
• Added: July, 2015
• Link: http://snpeff.sourceforge.net/SnpEff.html

See versions of snpeff which are available:

$ module avail snpeff

Notes from the sysadmin during installation:

$ cd /tmp
$ wget 'http://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip?r=&ts=1438066881&use_mirror=liquidtelecom' -O snpEff_latest_core.zip
$ unzip snpEff_latest_core.zip
$ sudo mkdir -p /export/apps/snpeff/4.1g
$ sudo cp -r snpEff/* /export/apps/snpeff/4.1g

Create shell script wrappers for snpEff.jar and SnpSift.jar, ie snpEff:

#!/bin/env bash

TOP=$(dirname $0)

# examples/examples.sh uses 4g heap
java -Xmx4g -jar $TOP/snpEff.jar $*