pgscatalog.calc 1.0.0a1

Libraries and applications for working with calculated polygenic scores

pgscatalog.calc

[!IMPORTANT]

• In 1.0.0-alpha.1 programs to calculate polygenic scores were added to this package
• The pgsc_calc load and pgsc_calc score programs are pre-release software that support basic PGS calculation only (chromosomes 1-22, indexed VCF and BGEN files, no ancestry adjustment)
• The simplest way to calculate polygenic scores with this software is to use v3 of the PGS Catalog Calculator
• Documentation for this package and more PGS calculation features will be added to future releases

This Python package contains:

• CLI applications to aggregate and adjust calculated polygenic scores (PGS) in the context of genetic ancestry similarity
• library classes and functions for working with calculated PGS and PCA data

Application	Description	Link
pgsc_calc load	Query an indexed VCF/BGEN and create a zarr zip archive	pgsc_calc load --help
pgsc_calc score	Calculate polygenic scores from zarr zip archives	pgsc_calc score --help
pgscatalog-aggregate	Aggregate calculated PGS split across multiple files	README
pgscatalog-ancestry-adjust	Adjust calculated PGS in the context of genetic ancestry	README

If you want to write Python code to work with PGS data, the library may be helpful for you.

Installation

or install via pip:

$ pipx install pgscatalog.calc

Documentation

Documentation is available at https://pygscatalog.readthedocs.io/.

Developer instructions

You'll need nox and uv installed.

To get set up with a development environment run:

$ nox -s dev
$ source .venv/bin/activate

This will create a virtual environment in the current directory.

$ pgscatalog-aggregate --help

nox can also be used to run tests and lint the package:

$ nox