Running Exomiser

Want help?

java -jar exomiser-cli-15.0.0.jar --help

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-15.0.0
java -jar exomiser-cli-15.0.0.jar analyse --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-15.0.0
java -jar exomiser-cli-15.0.0.jar analyse --sample examples/pfeiffer-family.yml --vcf examples/Pfeiffer-quartet.vcf.gz --assembly hg19 --ped examples/Pfeiffer-quartet.ped

By default there will be three 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 .jsonl, .parquet or .html e.g.

ls results/Pfeiffer*
results/Pfeiffer_exomiser.html  results/Pfeiffer_exomiser.jsonl results/Pfeiffer_exomiser.parquet

The HTML file is for human use, whilst the JSON file is better read by machines, for instance by using jq. The parquet file is a highly efficient binary file format to storing columnar data. It can be accessed using standard data tools like pandas, Polars or DuckDB. 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.

Running from alternate directory

If you’re running the exomiser from a different directory to the one the exomiser-cli-15.0.0.jar file is located, you will need to specify the path to the application.properties file in the start-up command. For example:

java -Dspring.config.location=/full/path/to/your/exomiser-cli/directory/application.properties -jar /full/path/to/your/exomiser-cli/directory/exomiser-cli-15.0.0.jar analyse --sample /full/path/to/your/exomiser-cli/directory/examples/pfeiffer-phenopacket.yml --vcf /full/path/to/your/exomiser-cli/directory/examples/Pfeiffer.vcf.gz --assembly hg19 --output-directory full/path/to/your/results/directory

n.b. the spring.config.location command must be provided using `-D` JVM system property before the -jar commands!