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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.



See versions of snpeff which are available:

$ module avail snpeff


Notes from the sysadmin during installation:

$ cd /tmp
$ wget '' -O
$ unzip
$ 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/ uses 4g heap
java -Xmx4g -jar $TOP/snpEff.jar $*
snpeff-software.txt · Last modified: 2017/02/11 09:10 by joguya