# ------------------------------------------------------ #
# GCTB v2.5.5 information
# Jian Zeng
# Date: 12/1/2026
# ------------------------------------------------------ #

GCTB is a software tool that comprises Bayesian mixed 
linear models for complex trait analyses using genome-wide 
SNPs. Version 2.5.5 includes genome-wide fine-mapping using SBayesRC (and SBayesR with the low-rank model).

Usage:

## Step 1. Generate eigen-decomposition data for SNPs matched in the GWAS summary statistics
gctb --ldm ukbEUR_13M_FullLDM --gwas-summary test.ma --make-ldm-eigen --thread 32 --out matched_ldm

## Step 2. Run genome-wide fine-mapping analysis using the SBayesRC model
gctb --gwfm RC --ldm-eigen matched_ldm --gwas-summary test.ma --annot annot.txt --gene-map gene_map.txt --thread 32 --out test


System
------

We provide a statically linked 64-bit Linux executable, 
gctb, that has been tested on several Linux systems. The
software has also been compiled and run on Mac operating
systems but this will require installation. 

Installation
------------

Please see https://github.com/jianzeng/GCTB for detailed
installation instructions.

Instructions for use
--------------------

Please see the tutorial on http://cnsgenomics.com/software/gctb
for a detailed description of how to run the summary-based 
components of the GCTB software on the demonstration data
derived from the 1000 Genomes.






 



