SnpEff and SnpSift are bundled toghether
Installing SnpEff is very easy, you just have to uncompress the ZIP fileHow 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.dirparameter). By default, this parameter points to the
datadirectory where you installed the tool (i.e. in unix systems, this is
./data). If you want to change this, you can edit the
snpEff.configfile and change the
#--- # 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
gitcommand 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
# 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.shto 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