LiteQTL is a package that runs whole genome QTL scans near real-time, utilizing the computation power of GPU.

LiteQTL uses new algorithms that enables near-real time whole genome QTL scans for up to 1 million traits. By using easily parallelizable operations including matrix multiplication, vectorized operations, and element-wise operations, our method is about 300 times faster than a R/qtl linear model genome scan using 16 threads.

Documentation

To find out more about methods used and also acceleration techniques, please refer to our paper on Biorxiv:

Chelsea Trotter, Hyeonju Kim, Gregory Farage, Pjotr Prins, Robert W. Williams, Karl W. Broman, and Saunak Sen.
Speeding up eQTL scans in the BXD population using GPUs.

Our package currently works for Julia v1.5 and v 1.6.

To add LiteQTL to your Julia installation:

julia> using Pkg;
julia> Pkg.add("LiteQTL")

To run the example provided by LiteQTL:

julia> using LiteQTL
julia> include(joinpath(pathof(LiteQTL), "../../example/spleen_analysis.jl"))

For more examples on how to use LiteQTL, please take a look at this example file.

• LiteQTL_Bin

This repo contais scripts to compile the LiteQTL package to remove the compilation time of Julia (the extra time in the first run in Julia REPL).

• LiteQTL G3 Supplement

It is an effort to make our research reproducible. All code related to experiment reuslt, from dowloading data, cleaning data, to running LiteQTL and creating figure are found in this repository. You can recreate the results in our paper Speeding up eQTL scans in the BXD population using GPUs using the scripts in this repository.