SnpEff

Download and install

SnpEff and SnpSift are bundled toghether

Download

Old versions here.



License

SnpEff is open source, released as "LGPLv3".

System requirements

SnpEff requires that you have Java v1.7 or later installed (any modern operating system has it).
The amount of memory used can vary significantly depending on genome size and data analysis type you are doing. For large genomes, such as the human genome, you'll probably need at least 4Gb of memory.

Installing SnpEff is very easy, you just have to uncompress the ZIP file

How to install using command line (unix systems):

It is better if you install SnpEff in snpEff directory in your home directory ($HOME/snpEff in unix systems).

# Go to home dir
cd

# Download latest version
wget http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip

# Unzip file
unzip snpEff_latest_core.zip

Configuration

In most cases you DO NOT need to configure anything.

The only configuration file is snpEff.config. Most configuration parameters, are explained in the comments in the same config file, so I won't repeat the explanation here :-)

Usually you do NOT need to change the configuration. Some peoeple may need to change the location of the databases (data.dir parameter). By default, this parameter points to the data directory where you installed the tool (i.e. in unix systems, this is ./data). If you want to change this, you can edit the snpEff.config file and change the data_dir entry:
#---
# Databases are stored here
# E.g.: Information for 'hg19' is stored in data_dir/hg19/
#
# You can use tilde ('~') as first character to refer to your home directory. 
# Also, a non-absolute path will be relative to config's file dir
# 
#---
data.dir = ./data/

In order to perform annotations, SnpEff automatically downloads and installs genomic database.

By default SnpEff automatically downloads and installs the database for you, so you don't need to do it manually.

Databases can be downloaded in three different ways:
  • The easiest way is to let SnpEff download and install databases automatically
  • You can pre-install databases manually using the 'SnpEff download' command (once SnpEff is installed). E.g. to donload the human genome database:

    java -jar snpEff.jar download GRCh38.76
    Note: Current human genome version at the time of writng is GRCh38.76.
  • Manual download: You can browse all available databases here. Make sure the database version matches your SnpEff version (e.g. do not use a 2.1 database with SnpEff 3..0).

There are over 20,000 databases available.

A list of databases is available in snpEff.config file.

You can also see all available databases by running the following command (once SnpEff has been installed):

java -jar snpEff.jar databases
Getting the souce: The source code is in GitHub (although we keep the binary distribution is at SourceForge). Here is the git command to check out the development version of the code:

git clone https://github.com/pcingola/SnpEff.git

# If you want to SnpSift as well
git clone https://github.com/pcingola/SnpSift.git

Install required libraries: Most libraries should be install using Maven, so you just need to run mvn command.

Intalling test cases: Test cases require special "test cases databases and genome", you can find them here:

# Install test databases in SnpEff's development directory (not the soruce code dir!)
cd $HOME/snpEff

# Download dtabases and genome for test cases
wget http://sourceforge.net/projects/snpeff/files/databases/test_cases.tgz

# Uncompress
tar -xvzf test_cases.tgz

# Go to Eclipse's workspace directory (where the source code is)
cd $HOME/workspace/SnpEff

# Create a link to the 'data' dir, so that we can run test cases within Eclipse
ln -s $HOME/snpEff/data

# Add data dir to 'gitignore'
echo "/data" >> .gitignore