SnpEff-Teaching

Category

Bioinformatics

Program On

Teaching

Version

4.3t

Author / Distributor

snpEff

Description

"SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes)." More details are at snpEff

Running Program

The last version of this application is at /usr/local/apps/eb/snpEff/4.3t-Java-1.8.0_144

To use this version, please load the module with

ml snpEff/4.3t-Java-1.8.0_144 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_snpEff
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=snpEff.%j.out
#SBATCH --error=snpEff.%j.err

cd $SLURM_SUBMIT_DIR
ml snpEff/4.3t-Java-1.8.0_144
java -jar snpEff.jar [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml snpEff/4.3t-Java-1.8.0_144 
java -jar snpEff.jar 
Error: Unable to access jarfile snpEff.jar

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Installation

Source code is obtained from snpEff

System

64-bit Linux