LiteQTL.jl Documentation

Package information

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

Features

Near real time computation for whole genome scan using Linear Model
Genome scan with covairates
CPU parallelization and GPU acceleration
Input data can be of different precisions (Float32, or Float64)

Input and Output

Input (all with no missing data)

Genotype probability
Phenotype
Covariates (Optional)

Output

(Default) Maximum LOD (Log of Odds) score, and the index of the maximum
LOD (Log of Odds) matrix

Example

We have created a Jupyter notebook with the whole analysis pipeline using the BXD spleen data as an example. Users can run eQTL scans and create a eQTL hits figure. See: example/spleen_analysis.ipynb

Auxilary Github Repositories

LiteQTL.jl Binary Compilation

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.jl G3 Journal Supplemental Materials

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.