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pgsc_calc v2.0.0-alpha
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@smlmbrt smlmbrt released this 07 Aug 16:14
· 139 commits to main since this release
v2.0.0-alpha
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Learn about vigilant mode.

This is the alpha release of the pgsc_calc pipeline's major new feature: to compare samples to a reference population in order to adjust PGS with genetic ancestry data (see documentation for details). The normal calculation of PGS is largely unaffected and directly comparable with previous versions of the calculator and PGS calculated with other tools.

Features

Major

  • Breaking changes to samplesheet structure to provide more flexible support for extra genomic file types in the future.
  • Genetic ancestry group similarity is calculated to a population reference panel (default: 1000 Genomes) when the --run_ancestry flag is supplied. This runs using PCA and projection implemented in the fraposa_pgsc (v0.1.0) package.
  • Calculated PGS can be adjusted for genetic ancestry using empirical PGS distributions from the most similar reference panel population or continuous PCA-based regressions.

These new features are optional and don't run in the default workflow.

Minor

  • Speed optimizations for PGS scoring (skipping allele frequency calculation). Thanks to @mglev1n for the suggestion!

Credits

Contributions from: @nebfield @smlmbrt @ens-lgil

Contributors

smlmbrt, ens-lgil, and 2 other contributors
Assets 2
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