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gwas-norm 0.3.0a0 documentation
gwas-norm 0.3.0a0 documentation

Setup

  • Getting Started with GWAS Normalisation
  • Setup a configuration file
  • Environment variables
  • Building the mapping files
  • Installing Ensembl VEP
  • Updating Ensembl VEP

GWAS normalisation

  • Overview and usage
    • The XML metadata file
    • Input file columns
    • The GWAS effect type
    • The GWAS analysis type
    • The directory structure of the normalised data
    • Output files

Variant mapping

  • Introduction to variant mapping
    • Running the Ensembl mapper on the command line
    • Using the Ensembl variant mapper API
    • INDEL normalisation

Programmer reference

  • Command-line endpoints
    • Python endpoints
    • BASH endpoints
  • gwas-norm API
    • gwas_norm package
    • gwas_norm.metadata sub-package
    • gwas_norm.utils sub-package
    • gwas_norm.variants sub-package
    • gwas_norm.variants.downloads sub-package
    • gwas_norm.hpc sub-package
  • Testing in GWAS norm

Project admin

  • Contributing to gwas-norm
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