1 Query phenotypes

  • First attempt link

2 Quality control

  • Population QC (based on UKB label and filter out outliers in PC space (10 PC’s)) link
  • Phenotype QC link
  • Monocyte technical covariates and multiple modes in monocyte count link

3 GWAS tries

  • First attempt link
  • Sanity check of GWAS runs using GCP link

4 Misc analysis

  • Splitting data into training, validation, and test sets link
  • REML link
  • REML on MESA models link
  • REML on 10 tissues CTIMP models (GTEx V8) link
  • REML on MESA models with common genes link

5 PRS/PTRS results

  • First look at PTRS/PRS on GTEx V8 whole blood CTIMP model link
  • MESA PTRS link
  • PTRS with LD block based pruning or mashr p-value link