The Pharmacogenomic Clinical Annotation Tool

View the Project on GitHub PharmGKB/PharmCAT

Pharmacogenomics Clinical Annotation Tool

An active area of genomic medicine implementation at many health care 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.


Refer to the project’s wiki on GitHub for documentation about the technical aspects of PharmCAT.

Read the PharmCAT wiki page on named allele matching to learn how PharmCAT matches genotype data to allele definitions.

There are detailed documents on how a few particular genes are handled by PharmCAT. See the gene definition exceptions for a rundown of exceptional circumstances when analyzing particular genes. The genes UGT1A1 and CFTR also have documentation of their non-standard allele matching algorithms.

HLA’s and G6PD are not included in the initial version of PharmCAT, see PMID: 31306493 for further explanations. The allele definition tables used in PharmCAT are based on CPIC allele definition tables from 2018. Newer guidelines (published after 2017) are NOT currently included in PharmCAT reports, covering additional genes RYR1, CACNA1S, NUTD15, CYP2B6 and recommendations for tamoxifen, atomoxetine, efavirenz, potent volatile anesthetic agents, succinylcholine and the DPYD update related to changes in recommendation for DPYD Intermediate Metabolizers. The CYP2D6 metabolizer grouping and the activity value for *10 are NOT updated to the newly released consensus metabolizer groups for CYP2D6.

Running PharmCAT

To learn how to run PharmCAT, read the instructions on GitHub. Please make sure to also read and understand PharmCAT’s VCF requirements.


If you’d like to view example input and output files generated by PharmCAT check out the examples page.


If you are interested in testing the tool or have questions, please contact



Teri Klein (Stanford University) and Marylyn Ritchie (University of Pennsylvania)

Current Team

Name Institution
Binglan Li Stanford University
Katrin Sangkuhl Stanford University
Mark Woon Stanford University
Michelle Whirl-Carrillo Stanford University
Ryan Whaley Stanford University
Yuki Bradford University of Pennsylvania
Scott Dudek University of Pennsylvania
Anastasia Lucas University of Pennsylvania
Sony Tuteja University of Pennsylvania
Anurag Verma University of Pennsylvania
Shefali Setia Verma University of Pennsylvania

Scientific Advisory Board

Burns Blaxall
Rhonda DeHoff
Phil Empey
Andrea Gaedigk
Houda Hachad
Jonathan Haines
James Hoffman
Janina Jeff
Stuart Scott
Casey Overby Taylor
Sara Van Driest
Marc Williams

Past Contributors

Name Institution
Solomon Adams University of Pittsburgh
Lester Carter Stanford (formerly)
Mark Dunnenberger Northshore University Health System
Philip Empey University of Pittsburgh
Alex Frase University of Pennsylvania
Robert Freimuth Mayo Clinic
Andrea Gaedigk Children’s Mercy Hospital
Adam Gordon University of Washington
Cyrine Haidar St Jude Children’s Research Hospital
James Hoffman St Jude Children’s Research Hospital
Kevin Hicks Moffitt Cancer Center & Research Institute
Ming Ta (Mike) Lee Geisinger
Neil Miller Children’s Mercy Hospital
Sean Mooney University of Washington
Minoli Perera Northwestern University
Thomas Person Geisinger
Josh Peterson Vanderbilt University
Stuart Scott Stanford University
Greyson Twist Children’s Mercy Hospital
Marc Williams Geisinger
Chunlei Wu Scrips Research Institute
Wenjian Yang St Jude Children’s Research Hospital