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snpeff-software

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

Usage

See versions of snpeff which are available:

$ module avail snpeff

Installation

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 $*
snpeff-software.txt · Last modified: 2017/02/11 12:10 by joguya