Kinship analysis was performed using KING (http://people.virginia.edu/~wc9c/KING/); principal component analyses were performed using EIGENSOFT (https://data.broadinstitute.org/alkesgroup/EIGENSOFT/); imputation was performed using EAGLE2 (https://data.broadinstitute.org/alkesgroup/Eagle/), Minimac3 (https://genome.sph.umich.edu/wiki/Minimac3), Sanger imputation server (https://imputation.sanger.ac.uk/), or RICOPILI (https://data.broadinstitute.org/mpg/ricopili/), depends on the sample; GWAS was performed using PLINK (https://www.coggenomics.org/plink2); meta-analyses was performed using METAL (https://genome.sph.umich.edu/wiki/METAL_Documentation); polygenic risk score analyses were performed using PRSice-2 (https://www.prsice.info/) or PRS-CS (https://github.com/getian107/PRScs); GCTA (https://cnsgenomics.com/software/gcta/#Overview) was used for identifying independent loci (GCTA-COJO), multi-trait conditional analysis (GCTA-mtCOJO), and Mendelian Randomization (GCTA-GSMR); LDSC (https://github.com/bulik/ldsc) was used for heritability estimate, genetic correlation analysis (also used LD-Hub, http://ldsc.broadinstitute.org/), and heritability enrichment analyses; FUMA (https://fuma.ctglab.nl/) was used for gene association, functional enrichment, and gene-set enrichment analyses; transcriptomic analyses were performed using S-PrediXcan and S-MultiXcan (https://github.com/hakyimlab/MetaXcan); PheWAS analyses were run using the PheWAS R package (https://github.com/PheWAS/PheWAS); Mendelian Randomization R Package (https://cran.rproject.org/web/packages/MendelianRandomization/index.html) and MR-PRESSO (https://github.com/rondolab/MR-PRESSO) were used for MR analyses; MTAG (https://github.com/omeed-maghzian/mtag) was used for Multiple trait analysis.
