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Determining Alleles

PharmCAT has an algorithm to match allele definitions to variant call data. The module in the PharmCAT responsible for this is the Named Allele Matcher. The Named Allele Matcher was written specifically for use in PharmCAT but can be run independently.

PharmCAT can also incorporate output from other diplotype calling software (e.g. Stargazer and StellarPGx). 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 Named Allele Matcher. See Outside Call Format for specifics.

For details on calling CYP2D6, plesae see Calling CYP2D6.


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