Running Exomiser
Usage
In general we recommend running Exomiser from the install directory. A single sample exome analysis can be run using the following command:
# run a test exome analysis cd exomiser-cli-14.0.0 java -jar exomiser-cli-14.0.0.jar --sample examples/pfeiffer-phenopacket.yml --vcf examples/Pfeiffer.vcf.gz --assembly hg19
This command prioritises variants from the input VCF file, called against the GRCh37/hg19 reference assembly in the context of the sample phenotypes encoded using Human Phenotype Ontology terms contained in the Phenopacket file.
Running a multi-sample VCF for trios also requires a PED file. e.g.
# run a test exome family analysis cd exomiser-cli-14.0.0 java -jar exomiser-cli-14.0.0.jar --sample examples/pfeiffer-family.yml --vcf examples/Pfeiffer-quartet.vcf.gz --assembly hg19 --ped examples/Pfeiffer-quartet.ped
By default there will be two output files written to the results
directory using the same filename as the input VCF file but
with _exomiser
appended before a file extension of .json
or .html
e.g.
ls results/Pfeiffer*
results/Pfeiffer_exomiser.html results/Pfeiffer_exomiser.json
The HTML file is for human use, whilst the JSON file is better read by machines, for instance by using jq. Details on how to interpret the output can be found in the Interpreting the Results section.
The examples
directory contains a selection of single sample exome and genome analysis files, a multisample (family)
analysis with an associated pedigree in PED
format, and the respective Phenopacket representations of the proband or
family.
Want help?
java -jar exomiser-cli-14.0.0.jar --help
Running from alternate directory
If you’re running the exomiser from a different directory to the one the exomiser-cli-14.0.0.jar file is located,
you will need to specify the path to the application.properties
file in the start-up command. For example:
java -Xmx4g -jar /full/path/to/your/exomiser-cli/directory/exomiser-cli-14.0.0.jar --analysis /full/path/to/your/exomiser-cli/directory/examples/test-analysis-exome.yml --spring.config.location=/full/path/to/your/exomiser-cli/directory/application.properties
n.b. the spring.config.location
command must be the last argument in the input commands!
Troubleshooting
java.lang.UnsupportedClassVersionError:
If you get the following error message:
Exception in thread "main" java.lang.UnsupportedClassVersionError:
org/monarchinitiative/exomiser/cli/Main : Unsupported major.minor version
or
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/monarchinitiative/exomiser/cli/Main has been
compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime
only recognizes class file versions up to 52.0
You are running an older unsupported version of Java. Exomiser requires java version 17 or higher. This can be checked by running:
$ java -version
You should see something like this in response:
openjdk version "17.0.9" 2023-10-17
OpenJDK Runtime Environment (build 17.0.9+9-Ubuntu-122.04)
OpenJDK 64-Bit Server VM (build 17.0.9+9-Ubuntu-122.04, mixed mode, sharing)
Versions lower than 17 (e.g. 1.5, 1.6, 1.7, 1.8, 9, 10) will not run exomiser, so you will need to install the latest java version.