Stars
Using real genotype data, simulate a complex trait as a function of latent expression, fit eQTL weights in independent data, and perform GWAS/TWAS on complex trait.
Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
R package for performing 2-sample MR using MR-Base database
Estimate local SNP heritability and genetic covariance from GWAS summary association statistics.