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GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. GCTA currently supports the following functionalities:

• Estimate the genetic relationship from genome-wide SNPs
• Estimate the inbreeding coefficient from genome-wide SNPs
• Estimate the variance explained by all the autosomal SNPs
• Partition the genetic variance onto individual chromosomes
• Estimate the genetic variance associated with the X-chromosome
• Test the effect of dosage compensation on genetic variance on the X-chromosome
• Predict the genome-wide additive genetic effects for individual subjects and for individual SNPs
• Estimate the LD structure encompassing a list of target SNPs
• Simulate GWAS data based upon the observed genotype data
• Convert Illumina raw genotype data into PLINK format
• Conditional & joint analysis of GWAS summary statistics without individual level genotype data
• Estimating the genetic correlation between two traits (diseases) using SNP data
• Mixed linear model association analysis

There may be multiple versions of GCTA available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail GCTA 

To select a module use

module load GCTA/[version]

where [version] is the version of choice.

GCTA is a multithreaded application. Make sure to match the number of cpus requested with the number of threads.

Environment variables set

• $PATH
• $GCTAHOME: location of test data

References

• J. Yang J, S. H. Lee, M. E. Goddard and P. M. Visscher PM. GCTA: a tool for Genome-wide Complex Trait Analysis. Am J Hum Genet. 2011, 76-82. Pubmed  |  PMC  |  Journal

Documentation

• Home page
• Manual
• Forum

Create a batch script similar to the following example:

#! /bin/bash
# this file is GCTA.batch
module load GCTA
gcta --bfile test --make-grm --out test

Submit to the queue with sbatch:

biowulf$ sbatch --cpus-per-task=1 --mem-per-cpus=2g GCTA.batch

Create a swarm command file similar to the following example:

# this file is GCTA.swarm
gcta --bfile test2 --make-grm --out test2
gcta --bfile test3 --make-grm --out test3
gcta --bfile test4 --make-grm --out test4

And submit to the queue with swarm

biowulf$ swarm -f GCTA.swarm --module GCTA -g 2

Allocate an interactive session with sinteractive and use as described above

biowulf$ sinteractive --mem=4g --cpus-per-task=2
node$ module load GCTA
node$ cp $GCTAHOME/test.* .
node$ gcta --bfile test --make-grm --out test
node$ exit
biowulf$