Our recommendation is to treat JER uncertainties as uncorrelated across all years in Run2.
NEW For analysis that are sensitive to JER, i.e. analyses that are able to constrain the single JER nuisance parameter per year w.r.t. their assigned uncertainty (e.g. using control regions), we provide a preliminary recipe to split uncertainties. A full breakup into sources was studied on 2018 data and is available for testing on request. For full Run2 analyses, we provide a simple breakup into 6 nuisance parameters per year (correlated among all jets in all events per year, but uncorrelated across years):
in region |eta| < 1.93 use one pT bin: (0,Inf)
in region 1.93 < |eta| < 2.5 use one pT bin: (0,Inf)
in region 2.5 < |eta| < 3 use two pT bins: (0,50) and (50,Inf)
in region 3 < |eta| < 5 use two pT bins: (0,50) and (50,Inf)