Skip to content

🧬 Running Exomiser from the Command Line

Goal

In this section we will install and run Exomiser CLI using the
Phenopacket generated with Phenoboard.

⚙️ Installation

Download the latest Exomiser distribution from:

👉 https://data.monarchinitiative.org/exomiser/latest/

At the time of writing, the file is:

exomiser-cli-14.0.0-distribution.zip

Required Data Files

You will also need:

  • Phenotype data — e.g. 2406_phenotype.zip
  • Variant data — choose hg19 or hg38

Workshop setup

For this workshop we will use the HG19 dataset because our example VCF file was made with this assembly.

⬇️ Download with wget

Create a project directory and download the files:

wget https://data.monarchinitiative.org/exomiser/latest/exomiser-cli-14.0.0-distribution.zip

# Download datasets (⚠️ ~40 GB total — this may take a long time!)
wget https://data.monarchinitiative.org/exomiser/latest/2406_hg19.zip
wget https://data.monarchinitiative.org/exomiser/latest/2406_phenotype.zip

Large download

The variant dataset is very large (~80 GB).
Ensure you have sufficient disk space and a stable internet connection.

From Europe, it may be quicker to use these links, which will download identical files.

2406_hg19 2406_hg38 2406_phenotype

Adjusting the versions

The version (e.g., version 2406 in 2406_hg19.zip) can be adjusted as needed. There might need to be some manual tweaking of the application.properties to select the correct exomiser.phenotype.data-version and exomiser.hg19.data-version.

📦 Unpack the Files

Unzip the distribution and data archives:

unzip exomiser-cli-14.0.0-distribution.zip
unzip 2402_*.zip -d exomiser-cli-14.0.0/data

This creates a directory named:

exomiser-cli-14.0.0/

📁 Expected Directory Structure

After extraction, your directory should look similar to this:

exomiser-cli-14.0.0/
├── CHANGELOG.md
├── LICENCE.txt
├── README.md
├── application.properties
├── examples
│   ├── Pfeiffer.vcf
│   ├── Pfeiffer.vcf.gz
│   ├── Pfeiffer.vcf.gz.tbi
│   ├── exome-analysis.yml
│   └── (...)
├── exomiser-cli-14.1.0.jar
├── lib
│   ├── HikariCP-5.0.1.jar
│   ├── (...)
│   └── xz-1.8.jar
├── pr2.json
└── results
    ├── bwa_mem2.gatk4_hc_gvcf.0037X64-N1-DNA1-WGS1-exomiser.html
    └── (...)

If everything has gone well, we can now run the softwre

java -Xmx4g -jar exomiser-cli-14.1.0.jar
usage: java -jar exomiser-cli-{build.version}.jar [...]
    --analysis <file>            Path to analysis script file. This should
                                 be in yaml format.
    (...)

Next Module: Java