▶️ Running Exomiser with a Phenopacket

In the previous step, we created a phenopacket for Pfeiffer syndrome using the
Phenoboard module.
We will now use this phenopacket as input for an Exomiser analysis.

🚀 Execute Exomiser

Run the following command from your terminal:

java -jar exomiser-cli-14.1.0.jar \
  --sample phenopacket.json \
  --vcf  examples/Pfeiffer.vcf \
  --assembly hg19

In this command,

• phenopacket.json is the phenopacket we made with Phenoboard (adjust the path/filename if needed)
• examples/Pfeiffer.vcf is an example Variant Call Format (VCF) file provided by the Exomiser distribution.

This should run for about 15 seconds and then produce an HTML output file.