Running PharmCAT

This will run the entire PharmCAT pipeline.

Building

If you checked out the repo, run:

> ./gradlew shadowJar

This will build a fat jar in build/libs.

Running

From the command line:

> java -jar build/libs/pharmcat-*-all.jar -vcf <sample_file> -o <output_dir>

Where:

• -vcf <sample_file> = required, sample VCF file
• -o <output_dir> = required, diretory path to write result files to
• -f <output_name> = optional, a base filename to use for output files (e.g. <output_name>.html)
• -a <astrolabe_file> = optional, gene call TSV file from the Astrolabe tool
• -k = optional, keep the interim output files from the NamedAlleleMatcher

Please make sure the VCF file complies with PharmCAT's VCF requirements.

Custom Data

PharmCAT includes the raw data it relies on. However, you can change this by using the following arguments:

• -g <guidelines_dir> = optional, directory containing JSON files of dosing guidelines instead of the default packaged guidelines
• -na <definitions_dir> = optional, a directory containing allele definitions to use instead of the default packaged allele definitions

The latest version of the dosing guideline annotations can be downloaded from PharmGKB.

Direct link: https://api.pharmgkb.org/v1/download/file/data/dosingGuidelines.json.zip?ref=pharmcat.