Welcome to the Pharmacogenetics Analysis Pipeline. This is a development repository and documentation containing instruction and technical discussion on the use of Pharmacogenetics Analysis Pipeline. This pipeline was created by Graeme Ford to perform the following core functions:

Perform VCF Spec validation
Merge multiple VCF datasets into one psudo-dataset*
Perform variant frequency analysis
Perform variant-effect-prediction

This work is licensed under a Creative Commons Attribution 4.0 International License.

Publications and Citations

Should you wish to cite this project or software, please select an apropriate paper/s from the list below:

Title: Pharmacogenetics of CYP2A6, CYP2B6, and UGT2B7 in the Context of HIV Treatments in African Populations
Date: 05 Dec 2022
DOI: 10.3390/jpm12122013
Abstract: Objectives: This study focuses on identifying variations in selected CYP genes related to treatment responses in patients with HIV in African populations by investigating variant characteristics and effects in African cohorts. Design: Cytochrome P450 (CYP) 2A6, 2B6, and Uridine 5’-diphospho-glucuronosyltransferase (UGT) 2B7 allele frequencies were studied using public-domain datasets obtained from the 1000 Genomes Phase 3 project, the African Genome Variation Project (AGVP), and the South African Human Genome Programme (SAHGP). Methods: Variant annotations were performed using...