A Toolkit to calculate Polygenic Scores (PGS) using PLINK2, PRSice2, RapidoGS, or PRS-CS.
The PGSToolKit acts as a wrapper tool for several PGS methods and can be used to compute polygenic scores for a target population using genome-wide association study (GWAS) summary statistics and a reference (e.g. 1000G phase 3). Current methods for computing polygenic scores require a wide range of different input formats and parameters. PGSToolKit provides a streamlined and clean alternative by using a fixed data format and parameters, configurable from a single configuration file. In short, a configuration file, pgstoolkit.conf, is set, and pgstoolkit.sh can be readily submitted to the server.
Current supported features are:
- Perform quality control by filtering variants based on imputation score and minor allele frequency.
- Compute polygenic scores using PRS-CS, RapidoPGS and PRSice2 based on GWAS summary statistics.
- Compute polygenic scores using the allelic score function of PLINK2 based on posterior variant effect sizes or weights.
Detailed instructions on using PGSToolKit can be found in the Wiki.
All scripts are annotated for debugging purposes - and future reference. PGSToolKit was tested within the context of a CentOS7 system with SLURM.
Copyright (c) 2017-2023 Sander W. van der Laan | s.w.vanderlaan [at] gmail [dot] com | vanderlaanand.science & Anton Ligterink.