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There is a discrepancy of the propagation of JES variations to type-1 MET between CMSSW and NanoAOD-tools. Discussed here:
https://indico.cern.ch/event/921037/contributions/3869620/attachments/2042217/3420993/nanoaod_jes_talk_v2.pdf
The fix was tested for 2017 (with METv2 recipe) and 2018. Consistent results up to the numerical precision of nanoAOD and the following bin migrations are now achieved.