Example 1 - All Reference

This is a collection of example files that demonstrate input and output files from a single run of PharmCAT. For more information about running PharmCAT, read the documentation.


First, a properly formatted single-sample VCF file with all positions specified.

This is an example of an optional file of outside diplotype calls. This one specifies a CYP2D6 call.


Named Allele Matcher output

The Named Allele Matcher component generates both HTML and JSON files with detailed information about how data in the sample VCF matches up with haplotype definitions.

Phenotyper output

The Phenotyper component takes data from the Named Allele Matcher and combines it with outside call data to assign function and metabolizer values.

Reporter output

The Reporter component takes data from the Phenotyper and matches phenotypes to information found in CPIC guideline data. This data is visible in an HTML report and also in a JSON file for machine parsing.

Example 2 - Some Non-Reference Alleles

This is a collection of example files with CYP2C19 *2/*2 and CYP2B6 *1/*6 diplotypes. One input VCF file that contains the source variant data and the corresponding output files that would result from running that input file.

Input VCF


PharmCAT is managed at Stanford University & University of Pennsylvania (NHGRI U24HG013077).