====== SnpEff & SnpSift ======
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.

===== Information =====

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

===== Usage =====

See versions of snpeff which are available:
<code>$ module avail snpeff</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>

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

<code>#!/bin/env bash

TOP=$(dirname $0)

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