Usage

In SnpEff-4.x series the upstream project provides a shell script snpEff, which can be used to run the program without calling java directly.

For snpeff/3.3h we provided a snpeff wrapper that made running snpeff easier.

For example, the below command:

java -Xmx2g -jar $HPC_SNPEFF_DIR/jar/snpEff.jar download -c $HPC_SNPEFF_CONF/snpEff.config -v athalianaTair10

could be run simply as:

snpeff download -v athalianaTair10

To override the default 2g java memory setting use the following command on the command-line or in a job script:

export _JAVA_OPTIONS="-Xmx4g"

Reference Databases

Note

We provide a full mirror of snpeff/4.2 reference databases released by the upstream project, so please do not request addition of a new reference database unless you need a custom database built from your data. Please provide a fasta file and an annotation file for building the custom database.