How to install and run SAIGE-QTL

Install SAIGE-QTL (current version 0.1.0 (updated on Nov 15 2023))

List of dependencies:

• R >= 3.6.1, gcc >= 5.4.0, cmake 3.14.1, cget, savvy
• R packages: Rcpp (>= 1.0.7), RcppArmadillo, RcppParallel, data.table, SPAtest (== 3.1.2), RcppEigen, Matrix, methods, BH, optparse, SKAT, qlcMatrix, RhpcBLASctl, roxygen2, rversions, devtools, dplyr, dbplyr

• Rscript ./extdata/install_packages.R can be used to install the R packages

• Two libraries for reading VCF files. Will be automatically installed during the SAIGE installation
• cget, savvy

Logs: