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→How to obtain PGx allele definitions from literature
* PGx alleles as VCF files from [https://www.pharmvar.org PharmVar]
PGx allele definitions are given in either GRCh37 or GRCh38 reference coordinates. The process of changing from GRCh37 to GRCh38 for PharmGKB seems to be only partially completed (at least in the JSON-LD data).
The allele definitions from the three sources are not always one-to-one, and some background knowledge about why this is, is required. Prefiltering of PharmGKB allele definitions were performed by the [[PGx in Estonia|PGx pipeline of the University of Tartu]] as shown in [https://www.biorxiv.org/content/early/2018/07/04/356204 ''Reisberg et al.''].
==How to define PGx alleles for next generation sequencing==