GCTA (Genome-wide Complex Trait Analysis) is designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits. GCTA was developed by Jian Yang, Hong Lee, Mike Goddard and Peter Visscher and is maintained in Peter Visscher's lab at the Queensland Institute of Medical Research.
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.
There are 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, type
module load GCTA/[ver]
where [ver] is the version of choice. This will set your $PATH variable to allow the gcta command.
To run GCTA:
$ cp $GCTAHOME/test.* . $ gcta --bfile test --make-grm --out testDocumentation