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Determining Alleles

PharmCAT has an algorithm to match allele definitions to variant call data. This algorithm in the PharmCAT codebase is called NamedAlleleMatcher. The NamedAlleleMatcher was written specifically for use in PharmCAT but can be run independantly.

PharmCAT can also incorporate output from other diplotype caller software (e.g. Astrolabe, Stargazer, etc…). These tools are run separately from PharmCAT but the results can be fed into PharmCAT to add unmatched genes or supercede diplotypes matched by PharmCAT’s NamedAlleleMatcher.

Currently, CYP2D6 diplotypes must be supplied by external caller software and the NamedAlleleMatcher is the default for all other gene diplotype matching.


PharmCAT is managed at Stanford University & University of Pennsylvania (NHGRI U24HG010862)