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This project is no longer under active maintenance. The allele definitions have not been updated since April 2020 which means allele calls may not match current definitions. See PharmVar for more information about allele definitions.
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A population-scale pharmacogenetic allele and phenotype caller

Greg McInnes and Adam Lavertu

If you find our code useful, please cite our paper.

Pharmacogenetics at scale: An analysis of the UK Biobank
Greg McInnes, Adam Lavertu, Katrin Sangkuhl, Teri E. Klein, Michelle Whirl-Carrillo, Russ B. Altman
Clinical Pharmacology and Therapeutics 2020/11/25; doi: https://doi.org/10.1002/cpt.2122

PGxPOP is a population-scale PGx allele caller designed to handle 100,000s of samples. Input is a phased VCF file, that has been indexed with tabix. Uses PGx allele definitions as developed by the original PharmCAT effort.

Installation:

PGxPOP requires Python 3.6 or greater

First, clone this repository to your local directory.

git clone https://github.com/PharmGKB/PGxPOP.git
cd PGxPOP
pip install -r requirements.txt

Once all the necessary requirement files have been installed, run using the following command:

python bin/PGxPOP.py --vcf <path/to/tabixed_vcf> -g <gene_name> --phased -o <path/to/output_dir>

You can also specify a genome build with the build flag:

python bin/PGxPOP.py --vcf <path/to/tabixed_vcf> -g <gene_name> --phased --build hg19 -o <path/to/output_dir>