SumTool | : hammer : Tool for GWAS summary-level data analysis | Machine Learning library

SumTool is a C++ library typically used in Artificial Intelligence, Machine Learning applications. SumTool has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

SumTool was designed to implement GWAS summary statistics analysis for big data. It can do ld, ldscore computation, ld pruning and clumping, linear model association, Zscore, Marginal effect imputation, summary data based SNP BLUP (SBLUP) solution, as well as LD regression for heritability and genetic correlation estimation. It is featured with memory efficiency and parallel computation. By the aid of package bigmemory, SumTool constructs memory-mapped files for genotype panel on disk instead of loading it all into Random Access Memory (RAM), which makes it possible to handle very big data with limited computation resources. Additionally, all matrix manipulations are enhanced by package RcppArmadillo, which could be sped up by intel MKL library on platform of Microsoft R Open (I suggest using MRO rather than R), and all loop procedures are accelerated by OpenMP technology. The functions of SumTool will keep on being enriched with more features based on users feedbacks. SumTool was developed by Lilin Yin with the support of Jian Zeng and Jian Yang. If you have any bug reports or questions, please feed back :point_right:here:point_left:.