LDpred2

Computing polygenic scores using LDpred2. prepare-corr: LD matrices for LDpred2 based on the 10K individuals in the validation set. prepare-genotypes: UKBB Europeans with imputed dosages for HapMap3 variants. This tutorial only uses fake data for educational purposes. You should also probably look at the code of the paper, particularly at the code to prepare summary statistics (including performing the quality control presented in the Methods section “Quality control of summary statistics” of the paper), at the code to read BGEN files into the data format used by bigsnpr, at the code to prepare LD matrices and at the code to run LDpred2 (genome-wide).