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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 latest installed version of Exomiser, simply load the exomiser module:

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

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

 A Tool to Annotate and Prioritize Exome Variants     v7.2.3

...

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 jobs

Here is an example job running with 1 core and 15G memory on nxv node:

#!/bin/bash
#$ -cwd
#$ -l h_rt=2:00:00
#$ -l h_vmem=15G
#$ -l node_type=nxv

module load exomiser/7.2.3

java -Xms2g -Xmx4g -jar $EXOMISER_JAR \
    --prioritiser hiphive \
    -I AD \
    -F 1 \
    --hpo-ids HP:0009773,HP:0010055,HP:0010669,HP:0011304 \
    -v $EXOMISER_HOME/data/Pfeiffer.vcf \
    --out-prefix results_hiphive

In this example exomiser is prioritising variants from an exome containing a spiked in causative mutation for Pfeiffer syndrome.

  • The exomiser is instructed to use the similarity matching algorithm contained in the hiPhive prioritiser --prioritiser hiphive.
  • Applying an autosomal dominant inheritance mode filter -I AD
  • Filtering out variants using a frequency cut-off of 1% -F 1
  • The patient phenotypes are described using the --hpo-ids argument
  • The input parameters tell exomiser to read in in the VCF file -v $EXOMISER_HOME/data/Pfeiffer.vcf
  • The output will be written to results_hiphive.html file --out-prefix results_hiphive

References