Download and install
SnpEff and SnpSift are bundled toghether
Download SnpEff Old versions here.
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
snpEff.config
.
Most configuration parameters, are explained in the comments in the same config file, so I won't repeat the explanation here :-)
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.
java -jar snpEff.jar download GRCh38.76Note: Current human genome version at the time of writng is GRCh38.76.
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
git
command to check out the development version of the code:
# Get SnpEff git clone https://github.com/pcingola/SnpEff.git # Get SnpSift as well git clone https://github.com/pcingola/SnpSift.git
mvn
command.
SnpEff/lib
)
# Go to 'lib' dir cd SnpEff/lib # Antlr mvn install:install-file \ -Dfile=antlr-4.5.1-complete.jar \ -DgroupId=org.antlr \ -DartifactId=antlr \ -Dversion=4.5.1 \ -Dpackaging=jar # BioJava core mvn install:install-file \ -Dfile=biojava3-core-3.0.7.jar \ -DgroupId=org.biojava \ -DartifactId=biojava3-core \ -Dversion=3.0.7 \ -Dpackaging=jar # BioJava structure mvn install:install-file \ -Dfile=biojava3-structure-3.0.7.jar \ -DgroupId=org.biojava \ -DartifactId=biojava3-structure \ -Dversion=3.0.7 \ -Dpackaging=jarOnce the libraries are installed, you can use
make.sh
to build the code
cd $HOME/snpEff # Create link to scripts_build directory if it doesn't exist ln -s $HOME/workspace/SnpEff/scripts_build # Invoke the build script ./scripts_build/make.sh
# 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