The PharmCAT tool is really a pipeline comprised of multiple modules:
VCF Preprocessor module is responsible for normalizing the input VCF. See VCF Preprocessor for details.
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
Phenotyper module is reponsible for translating diplotypes and other genotype information into gene-specific phenotypes. For example, CYP2C19
*2/*4 is a poor metabolizer.
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