PharmCAT

August 4, 2025 · View on GitHub

PharmCAT CI Preprocessor CI codecov.io

PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics tool that analyzes genetic variants to predict drug response and tailor medical treatment to an individual patient’s genetic profile. It does this in two phases:

  1. Processes VCF files from next generation sequencing (NGS) or genotyping methods and identifies pharmacogenomic (PGx) genotypes and infers haplotypes, typically called star alleles.
  2. Uses the pharmacogene diplotypes (combination of maternal and paternal star alleles) to predict PGx phenotypes and reports the corresponding drug-prescribing recommendations from CPIC guidelines, ClinPGx-annotated DPWG guidelines and ClinPGx-annotated FDA-approved drug labels.

For more information:

Status

PharmCAT is available for general use, but it is still under active development. New features, data updates, and bug fixes will be released. Watch this repository or check the releases page for new releases.

All technical requirements and documentation are available on PharmCAT.org.

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

Contact

For technical questions or bug reports, file an issue.

For general questions about the PharmCAT project, contact pharmcat@clinpgx.org.

Liability

:warning: PharmCAT assumes no responsibility for any injury to person or damage to persons or property arising out of, or related to any use of PharmCAT, or for any errors or omissions. The user recognizes they are using PharmCAT at their own risk.