PharmCAT Modules

The PharmCAT tool is really a pipeline comprised of multiple modules:

The VCF Preprocessor module is responsible for normalizing the input VCF. See VCF Preprocessor for details.

The Named Allele Matcher module is responsible for calling diplotypes for a sample based on a VCF file. For an overview on how this works, see Named Allele Matcher 101

The Phenotyper module is reponsible for translating diplotypes and other genotype information into gene-specific phenotypes. For example, CYP2C19 *2/*4 is a poor metabolizer.

The Reporter module is responsible for generating a report with genotype-specific expert-reviewed drug prescribing recommendations for clinical decision support.

See Matching Recommendations for details on how the Phenotyper and Reporter works.

process diagram

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