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→Chosing an appropriate genomic reference build
==How to chose the correct PGx allele definitions==
===Chosing an appropriate genomic reference build===
PGx allele definitions are given in either GRCh37 or GRCh38 reference coordinates. PharmCAT, CPIC and PharmGKB as a rule use build GRCh38. The process of changing from GRCh37 to GRCh38 for the PharmGKB API seems to be only partially completed. For instance, in the PharmGKB API JSON-LD data, the build is given as "hg38", but the actual coordinates are mostly GRCh37 (hg19). In the PharmGKB and CPIC Excel sheets, the move to GRCh38 is completed.As is evident from liftOver, hg19 is not equal to GRCHh37, nor hg38 to GRCHh38. Are we sure that there are no errors here?
===Chosing the correct variants to include in the PGx alleles===
The allele definitions from PharmGKB and PharmVar are not always one-to-one, and some background knowledge about why this is, is required.