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