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Running PharmCAT

Ryan Whaley edited this page Oct 26, 2018 · 11 revisions

This will run the entire PharmCAT tool.


You will need Java 1.8. This was developed and run on the official Oracle JDK.

You will also need to have Gradle installed to compile PharmCAT.


If you checked out the repo, run:

> ./gradlew shadowJar

This will build a fat jar in build/libs.

For more information on building PharmCAT, check Building PharmCAT.


From the command line:

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

note: the * is not literal above, it's used in place of whatever version of PharmCAT you want to run. For example, a specific version could be pharmcat-0.2.0-all.jar.


  • -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
  • -j = optional, file path to write JSON version of report data to

:warning: 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.

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