GCTB

Genome-wide Complex Trait Bayesian analysis

Overview

GCTB is a C++ software tool that comprises Bayesian mixed linear models for complex trait analyses using genome-wide SNPs.

How to compile GCTB 1.0

GCTB 1.0 has dependencies on two C++ libraries i.e. Eigen3 and Boost.

To compile GCTB 1.0 on a Linux/Mac system, follow below steps:

1. Download Eigen3 and Boost;
2. Edit their path in the enclosed Makefile (these two libraries themselves do not need to be compiled);
3. Switch “SYS” to “LINUX” or “MAC” in the Makefile;
4. Execute make command.

We have also included a Xcode (v7.3.1) project file for Mac system. To compile in the Xcode, follow below steps:

1. Click on the project in Xcode and then click on Build Settings;
2. Add “/usr/local/include” to “Search Paths – Header Search Paths”;
3. Add the paths of Eigen and Boost libraries to “Search Paths – Header Search Paths”;
4. Use Command+B to compile.

How to run GCTB 1.0

Use the command below (with the test dataset):

gctb --bfile data/1000G_eur_chr22 --pheno data/test.phen --bayes S --chain-length 1100 --burn-in 100 --out test

An alternative way to run the program with the parameter settings is to use a input parameter file:

gctb --inp-file test.inp