Contains Lavinia's WORK IN PROGRESS UKBB scripts for GWAS
biobank_reformat.sh : contains all the scripts used to make the various input files. Once checked and options are decided on this will be fixed and people won't need to access this file. The only exception is that people may choose to submit their own exclusion or modelSNPs lists, though separate guidance can be given on how they should do this.
UKBB_GWAS_01.sh : This is the BOLT-LMM script for CHR1, needs some refinement, some options tweakable by user and rolling out across other chromosomes.
For more info on pipeline, see google doc: https://docs.google.com/document/d/1Xsq0DiFzOdKpFo02IhyIv7FVnqJbPIRwWn4hRoguNFY/edit
Scripts currently contain some paths to my own directory, Equivalent files are also available in: /projects/MRC-IEU/groups/biobank/derived/Lavinia/