We used the Eagle2 software56 [https://data.broadinstitute.org/alkesgroup/Eagle] for pre-phasing and Minimac357 [https://genome.sph.umich.edu/wiki/Minimac3] for imputation in the Partners Biobank European sample. Lastly, we removed markers with MAF <1%, missing rate >2%, imputation quality INFO score <0.8, and significant deviation from HWE with P < 1 × 10−10. All genetic analyses in the Partners Biobank were conducted using PLINK 1.954.
