Pharmacogenomics Clinical Annotation Tool

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An active area of genomic medicine implementation at many healthcare organizations and academic medical centers includes development of decision support and return of results around pharmacogenomics. One of the challenges in implementing pharmacogenomics is the representation of the information in clinical dosing guidelines, including star-allele haplotypes, and extracting these variants and haplotypes from genetic datasets. In a collaboration between the Pharmacogenomics Knowledgebase (PharmGKB) and the former PGRN Statistical Analysis Resource (P-STAR), with input from other groups, we are developing a software tool to extract guideline variants from a genetic dataset (represented as a vcf), interpret the variant alleles, and generate a report with genotype-based prescribing recommendations which can be used to inform treatment decisions.

The Clinical Pharmacogenetics Implementation Consortium (CPIC) has established guidelines surrounding gene-drug pairs that can and should lead to treatment modifications based on genetic variants. These guidelines are used for the initial version of PharmCAT, and other sources of PGx information and guidelines will be included in the future.


PharmCAT is under active development.

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See Genes & Drugs for a list of all genes and drugs supported by PharmCAT. We have detailed documentation in Gene Definition Exceptions for genes that require special handling.

Read the Methods to learn how PharmCAT works, including how it matches sample data to allele definitions and matches genotypes to drug recommendations.

Running PharmCAT

Learn how to run PharmCAT and all the different components that make up the PharmCAT tool. Please make sure to also read and understand PharmCAT's VCF requirements.

Tutorial videos are available on the PharmGKB YouTube channel. These videos provide step-by-step demonstrations on running PharmCAT. The first two videos cover:

  1. An introduction to PharmCAT, modules, and reports
  2. How to run PharmCAT - a hands-on example that walks through the setup and running PharmCAT

Future videos will cover more topics.


PharmCAT is licensed under the Mozilla Public License 2.0 (MPL-2.0).


We have an example collection of synthetic input and output files generated by PharmCAT.

View examples of input and output files.

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