snpEff is a genetic variant annotation, and functional effect prediction tool.


Configuration File

snpEff requires a one-off configuration of the .config file. The following instructions are a one-off set up of the configuration file required for snpEff.

  1. Load the latest version of the snpEff module.
  2. Make a copy of the snpEff config file, replacing <project_id>, with your project ID.
    cp $EBROOTSNPEFF/snpEff.config /nesi/project/<project_id>/my_snpEff.config
  3. Open themy_snpEff.config file, and edit line 17 from the top to point to a preferred path within your project directory or home directory, e.g., edit line 17 data.dir = ./data/ to something like:data.dir =/nesi/project/<project_id>
    Please note that you must have read and write permissions to this directory.
  4. Run snpEff.jar using the -c flag to point to your new config file, e.g., -c path/to/snpEff/my_snpEff.config For example:
    java -jar $EBROOTSNPEFF/snpEff.jar -c /nesi/project/<project_id>/my_snpEff.config


Example Script

You will need to set up your configuration file before you run snpEff.

#!/bin/bash -e

#SBATCH --account nesi12345
#SBATCH --job-name my_snp_EFF_job
#SBATCH --time 20:00
#SBATCH --memory 4G
#SBATCH --output %x_%j.out # Name output file according to job name with Job ID

# purge all other modules that have already been loaded
module purge

# load specific snpEff version
module load snpEff/5.0-Java-11.0.4

# bring up help menu
java -jar $EBROOTSNPEFF/snpEff.jar -h

# run snpEff
java -jar $EBROOTSNPEFF/snpEff.jar -c /nesi/project/<project_id>/my_snpEff.config <other flags>


Was this article helpful?
0 out of 0 found this helpful