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→How to obtain PGx allele definitions from literature
PGx alleles are collected and distributed through various channels
* PGx alleles on JSON-LD format from the [https://api.pharmgkb.org PharmGKB API]
* PGx alleles on Excel-style formats from the PGRN Translational Pharmacogenetics Project (TPP), published also accessible through the [https://api.pharmgkb.org PharmGKB API]
* 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 is seems to be only partially completed(at least in the JSON-LD data).We suspect that there The allele definitions from the three sources are serious discrepancies between PharmVar not always one-to-one, and PharmGKB sources (which some background knowledge about why this is, is strange as PharmGKB gets data form PharmVar).required
==How to define PGx alleles for next generation sequencing==