PharmCAT

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The Pharmacogenomic Clinical Annotation Tool

View the Project on GitHub PharmGKB/PharmCAT

Example Report

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

Input

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.

Output

NamedAlleleMatcher output

The NamedAlleleMatcher 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 NamedAlleleMatcher 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.