Contents

  • Home
  • Getting started
  • How-to guides
  • Reference guide
    • Input Parameters/Flags
    • Samplesheet schema
    • Containers
  • Outputs & results
  • Troubleshooting
  • Glossary

About the project

  • Changelog
  • License

Useful links

  • PGS Catalog
  • pgsc_calc Github
    • Issue tracker
  • pgscatalog_utils Github

Index
  • .rst
Contents
  • Calculating polygenic scores
  • Making genomic data and scorefiles compatible
  • Working in different environments
  • Working with complex datasets

How-to guides

Contents

  • Calculating polygenic scores
  • Making genomic data and scorefiles compatible
  • Working in different environments
  • Working with complex datasets

How-to guides#

Calculating polygenic scores#

  • How do I prepare my input genomes?
  • How to set up a samplesheet
  • How to use scoring files in the PGS Catalog
  • How to apply multiple scores in parallel

Making genomic data and scorefiles compatible#

  • How to use a custom scoring file
  • How to liftover scoring files to match your input genome build
  • How to set effect type of variants in a scoring file

Working in different environments#

  • How do I run pgsc_calc on larger datasets and more powerful computers?
  • How do I run the pipeline on an M1 Mac?

Working with complex datasets#

  • How to get a copy of the standardised genomic data
  • How to set parameters in a file

© Copyright Polygenic Score (PGS) Catalog team (licensed under Apache License V2).