Skip to content

Latest commit

 

History

History
37 lines (29 loc) · 2.74 KB

README.md

File metadata and controls

37 lines (29 loc) · 2.74 KB
Raw

ukbb-tools

This repository contains our complete set of tools for preprocessing, quality control, and preliminary analyses on UK Biobank data. There is a folder in the repo per set of methods as defined in the Table of Contents below. Each subdirectory has a README.md file that should be read before use. These files detail how to use all files within the directory.

Contents

  1. Preprocessing
  2. Phenotyping
  3. Filtering
  4. GWAS
  5. GBE
  6. PheWAS
  7. LD score regression (LDSC)
  8. UK Biobank Bulk Download
  9. Flip-check, flip-fix, and coordinate lift over w/ UCSC liftOver
  10. Biomarker Adjustment
  11. GREAT Enrichment
  12. SciDB Query for PheWAS
  13. Multiple Rare-variants and Phenotypes (MRP) - Rare-variant signal aggregator
  14. LD map and LD pruning
  15. Genetic Relationship Matrix calculation (GRM via GCTA)
  16. snpnet (Large-scale Cox Proportional Hazards)
  17. VEP Variant Annotation
  18. Meta-analysis with METAL
  19. Multiple Rare-variants and Phenotypes Mixed Model (MRPMM)

The ukbb-tools module on Sherlock

All this code has been ported to a module on Sherlock. Click for more details on how to load and use this module.

There is an updater script that pushes your current directory - use with appropriate caution, as it takes the master branch - and makes it a version of the module. The only argument for the updater is a date; this is used as a version label.

Example Usage:

bash ukbb-tools.module.updater.sh 20200225