SnpEff and SnpSift are bundled toghether
SnpEff requires genomic databases
(see next section)
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:
# 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
In order to perform annotations, SnpEff requires a genomic database.Databases can be downloaded in two different ways:
java -jar snpEff.jar download GRCh37.69Note: Current human genome version at the time of writng is GRCh37.69.
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Warning: This list might be outdated, taka a look at the previous section on how to obtain an updated list of databases.