Running PharmCAT

This will run the entire PharmCAT tool.

Requirements

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

You can either build a fresh copy of the Jar file yourself or download a pre-compiled Jar file from our releases page.

You will need to have Gradle installed to compile PharmCAT.

Checkout the repo and from the base repo directory run:

> ./gradlew shadowJar

This will build a "fat" jar with bundled dependencies in build/libs. You can use this jar file in the following section.

For more information on building PharmCAT, check Building PharmCAT.

From the command line:

> java -jar <path_to_jar_file> -vcf <sample_file> -o <output_dir>

Where:

-jar <path_to_jar_file> = required, the compiled PharmCAT Jar file
-vcf <sample_file> = required, sample VCF file (:warning: Please read VCF requirements)
-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 <outside_call_file> = optional, gene call TSV file from the an outside tool (like Astrolabe)
-k = optional, keep the interim output files from the NamedAlleleMatcher
-j = optional, flag to write reporter JSON data (will be <output_name>.report.json)
-pj = optional, flag to write phenotyper JSON data (will be <output_name>.phenotyper.json)

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

-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.