pgscatalog-utils

This convenience package bundles every PGS Catalog application, including:

Application Description Link
pgscatalog-download Download scoring files from the PGS Catalog in specific genome builds README
pgscatalog-combine Combine multiple scoring files into a consistent structure README
pgscatalog-relabel Relabel values in a column based on values in a column in another file README
pgscatalog-match Match structured scoring file to variants in target genomes README
pgscatalog-matchmerge Merge variant match results, useful on larger datasets README
pgscatalog-intersect Match variants across two different variant information files (e.g. reference & target genomes) README
pgscatalog-aggregate Aggregate calculated PGS split across multiple files README
pgscatalog-ancestry-adjust Adjust calculated PGS in the context of genetic ancestry README

Please note v1.0.0 contains breaking changes: CLI applications have been renamed and the package has been significantly refactored.

See https://github.com/PGScatalog/pygscatalog for more details.

Installation

install with bioconda

or install via pip:

$ pipx install pgscatalog-utils

Documentation

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

Key dates

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  • Released:
Newer release available (2.0.4)

Owner

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2 maintainers

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Credits

Author: Benjamin Wingfield

License

Apache Software License (Apache-2.0)

Requires

Python >=3.10

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