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Exomiser

The Exomiser is a program for finding potential disease-causing variants from whole exome sequence analysis or whole genome sequencing data.

Exomiser is available as a module on Apocrita.

Usage

To run the default installed version of Exomiser, simply load the exomiser module:

$ module load exomiser
$ java -jar $EXOMISER_JAR
...

 Welcome to:
  _____ _            _____                     _
 |_   _| |__   ___  | ____|_  _____  _ __ ___ (_)___  ___ _ __
   | | | '_ \ / _ \ |  _| \ \/ / _ \| '_ ` _ \| / __|/ _ \ '__|
   | | | | | |  __/ | |___ >  < (_) | | | | | | \__ \  __/ |
   |_| |_| |_|\___| |_____/_/\_\___/|_| |_| |_|_|___/\___|_|

...

For more information, pass the --help switch (i.e. java -jar $EXOMISER_JAR --help).

For your convenience, the Exomiser module sets two variables:

  • EXOMISER_JAR - Contains the full path to the main binary .jar file
  • EXOMISER_DIR - Contains the full Exomiser directory path.

Example job

Serial job

Here is an example job running on 1 core and 1G of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load exomiser

java -jar $EXOMISER_JAR --analysis example.yaml

References