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→Chosing the correct variants to include in the PGx alleles
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.
===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. Prefiltering of PharmGKB allele definitions was performed by the [[PGx in Estonia|PGx pipeline of the University of Tartu]], although the exact prefiltering was not published in the supplementary material to [https://www.biorxiv.org/content/early/2018/07/04/356204 ''Reisberg et al.''].
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