Calculate polygenic scores locally

We help to develop many polygenic score (PGS) tools which are open source, permissively licensed, and can run in your local environment. This means it's always possible to bring our code to your data.

The PGS Catalog Calculator

The PGS Catalog Calculator (pgsc_calc) is a bioinformatics best-practice analysis pipeline for calculating polygenic [risk] scores on samples with imputed genotypes using existing scoring files from the PGS Catalog and/or user-defined PGS/PRS.

When users upload target genomes to the GeneticScores.org calculation service it uses pgsc_calc to calculate and adjust PGS.

pygscatalog

This repository contains Python applications and libraries for working with polygenic scores and the PGS Catalog, an open database of polygenic scores and the relevant metadata required for accurate application and evaluation.

pgsc_calc uses these applications internally.

pgsc_benchmark

The pgsc_benchmark tool aims to facilitate the widespread performance benchmarking of polygenic scores curated in the PGS Catalog. It has been designed to run directly on the output files produced by the PGS Catalog Calculator, providing a reproducible method for evaluating score performance. Users are able to run the tool using their own study cohorts and phenotype data, generating a consistent and directly comparable set of performance metrics across all desired PGS.