SnpEff for Spritz

This fork of SnpEff has been adapted for proteogenomics to be used in Spritz.

SnpEff Documentation

http://snpeff.sourceforge.net/

Enjoy!

Pablo Cingolani

Usage example

1. Please download the latest release
2. Once unzipped, this folder should have the file snpEff.jar binary in its base directory.
3. You can then use commands such as those used in Spritz to generate a proteogenomic database for variants, e.g., java -Xmx16000M -jar snpEff.jar -v -nostats -fastaProt output.protfa -xmlProt output.protxml reference.gff3 input.vcf > output.ann 2> log.txt

Building information (as of June 2020)

To build SnpEff for Spritz:

1. Activate spritz conda environment
2. conda install maven
3. Execute the following commands:

cd SnpEff
mvn install:install-file -Dfile=lib/antlr-4.5.1-complete.jar -DgroupId=org.antlr -DartifactId=antlr -Dversion=4.5.1 -Dpackaging=jar
mvn install:install-file -Dfile=lib/biojava3-core-3.0.7.jar -DgroupId=org.biojava -DartifactId=biojava3-core -Dversion=3.0.7 -Dpackaging=jar
mvn install:install-file -Dfile=lib/biojava3-structure-3.0.7.jar -DgroupId=org.biojava -DartifactId=biojava3-structure -Dversion=3.0.7 -Dpackaging=jar
export VERSION=4.3
export VERSION_UND=`echo $VERSION | tr '.' '_'`
mvn clean compile assembly:assembly
mvn install:install-file -Dfile=target/SnpEff-$VERSION.jar -DgroupId=org.snpeff -DartifactId=SnpEff -Dversion=$VERSION -Dpackaging=jar -DgeneratePom=true --quiet
cp target/SnpEff-$VERSION-jar-with-dependencies.jar snpEff.jar
cd ..

4. To create new zip-file release, include everything except the data folder.