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Running the NamedAlleleMatcher

Ryan Whaley edited this page Oct 26, 2018 · 6 revisions

This will run the first half of the PharmCAT tool. The results of the NamedAlleleMatcher should be fed to the Reporter.


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


If you checked out the repo, run:

> ./gradlew shadowJar

This will build a fat jar in build/libs.


From the command line:

> java -cp build/libs/pharmcat-*-all.jar org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher -vcf <vcf_file> -html <html_file>


  • -vcf <sample_file> = required, sample VCF file
  • -html <html_file> = optional, the HTML file to write the results to
  • -json <json_file> = optional, the JSON file to write the results to

Custom Data

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

  • -d <definitions_dir> = optional, a directory containing allele definitions to use instead of the default packaged allele definitions
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