kenhanscombe / pgxpop

PGxPOP

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>