snpeff-software
Table of Contents
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
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 09:10 by joguya