/PharmCAT

The Pharmacogenomic Clinical Annotation Tool

Primary LanguageJavaMozilla Public License 2.0MPL-2.0

PharmCAT

PharmCAT CI Preprocessor CI codecov.io

A tool to extract all CPIC guideline gene variants from a genetic dataset (represented as a VCF file), interpret the variant alleles, and generate a report.

For more details:

  1. Go to PharmCAT website
  2. Read the PharmGKB blog post about PharmCAT
  3. Read the article on GenomeWeb

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 repo 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 U24HG010862)

Contact

For technical questions or bug reports, file an issue.

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

Liability

⚠️ PhamCAT 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.