SnpEff

Download and install

SnpEff and SnpSift are bundled toghether

Download

SnpEff requires genomic databases
(see next section)

Old SnpEff, SnpSift and database versions can be found here.

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

It is prefered that you install SnpEff in snpEff directory in your home directory. Otherwise, you must update the data_dir parameter in your snpEff.config file.

How to install:
  • Unix & OS.X: You can open a terminal and run the following commands
    # Got o home dir
    cd
    
    # Download latest version
    wget http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip
    
    # Unzip file
    unzip snpEff_latest_core.zip
    
  • Windows: Double click on the snpEff_latest_core.zip and copy the contents to the directory of your choice.


Remember to update data_dir parameter in your snpEff.config file.

In order to perform annotations, SnpEff requires a genomic database.

Databases can be downloaded in two different ways:
  • The easiest way to download a SnpEff database is to use the 'download' command (once SnpEff is installed). E.g. to donload the human genome database:

    java -jar snpEff.jar download GRCh37.69
    Note: Current human genome version at the time of writng is GRCh37.69.
  • 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 2,500 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

Here is a list of currently available database

Warning: This list might be outdated, taka a look at the previous section on how to obtain an updated list of databases.