Core analysis code for RICOPILI can be found at “https://sites.google.com/a/broadinstitute.org/ricopili/”. This wraps PLINK (“https://www.cog-genomics.org/plink2/”), EIGENSOFT (“https://www.hsph.harvard.edu/alkes-price/software/”), EAGLE2 (“https://alkesgroup.broadinstitute.org/Eagle/”), MINIMAC3 (“https://genome.sph.umich.edu/wiki/Minimac3”), SHAPEIT3 (“https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html”), METAL (“https://genome.sph.umich.edu/wiki/METAL_Documentation”), LDSR (“https://github.com/bulik/ldsc”). For downstream analyses, FINEMAP can be found at “http://christianbenner.com/”, and our utility for meta-analysing cohort-specific LD matrices can be found at https://github.com/Pintaius/LDmergeFM. MAGMA can be found at ”https://ctg.cncr.nl/software/magma” and the GO gene sets and automated curation pipeline are provided in https://github.com/janetcharwood/pgc3-scz_wg-genesets. SMR is available at “https://cnsgenomics.com/software/smr/” and SbayesS at “https://cnsgenomics.com/software/gctb/”.
