Zenome Pharmacogenomics caller for mixed NGS data (WES + LP WGS), forked from StellarPGx
CYP450 genes supported: CYP2D6, CYP2B6, CYP2C19, CYP2C9, CYP3A4, CYP3A5, CYP1A2
Non-CYP450 genes supported: CYPOR (POR)
Zenomix is based on StellarPGx (please refer to the excellent documentation here). Main script is built using PHP and utilize Docker technology.
The program is focused on analysis of short-read high-coverage whole exome sequence data in combination with low-coverage(2-7x) whole genome sequence data. To analyze hybrid alleles in such complicated gene as CYP2D6, we developed hybrid algorithm that extracts reads from certain parts of paralog, which has high homology to the target gene. Developed especially to analyze the metabolism of drugs used in psychiatry. 7 determined cytochromes are involved in the inactivation of more than 95% of all known psychiatric drugs. Cytochrome P450 Oxidoreductase donate electrons directly from NADPH to all microsomal P450 enzymes. Therefore, impaired POR function can alter the metabolism of all P450 cytochromes.
The following are required to run the Zenomix pipeline:
- Prerequisite software
- PHP (preferably v8.x)
- Docker
- Whole genome sequence (WGS) data
- Indexed BAM/CRAM files
- Reference genome
- hg19, b37, or hg38
Install PHP on Linux by running the following command (Skip if you have PHP installed already):
sudo apt-get install php
For Docker installation, please refer to the excellent documentation here)
Clone the StellarPGx repository by running the following command:
git clone https://github.com/zenomeplatform/pharm_pipe.git && cd pharm_pipe
The parameters for Docker are set as default.
For execution on a local machine
php -f run_zenomix.php ref_file bam_path bam_name work_mode report_path