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Sander W. van der Laan edited this page Aug 16, 2024 · 3 revisions

Welcome to the PGSToolKit wiki

The PGSToolKit acts as a wrapper tool for several methods and can be used to compute polygenic scores (PGS) for a target population. Current methods for computing polygenic scores require a wide range of different input formats and parameters. This toolkit provides a streamlined and clean alternative by using a fixed data format and parameters, configurable from a single configuration file.

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 SNP effect sizes.
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