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GCTA specifications


Unique identifier OMICS_04898
Alternative name Genome-wide Complex Trait Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.24
Stability Stable
Maintained Yes


No version available

Publication for Genome-wide Complex Trait Analysis

GCTA citations


Thirty loci identified for heart rate response to exercise and recovery implicate autonomic nervous system

Nat Commun
PMCID: 5955978
PMID: 29769521
DOI: 10.1038/s41467-018-04148-1

[…] To examine the existence of independent SNPs to lead SNPs, we applied genome-wide complex trait analysis (GCTA) for all validated and genome-wide significant loci from the full data set GWAS. A secondary signal would be declared if: (i) the newly identified SNP original […]


Cross ancestry genome wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

Nat Commun
PMCID: 5951816
PMID: 29760442
DOI: 10.1038/s41467-018-03646-6

[…] We applied the conditional and joint (CoJo) analysis approach implemented in the software Genome-wide Complex Trait Analysis (GCTA) on European-specific meta-analysis results in order to identify potentially independent signals within the same genomic regions. For this CoJo analysis we use […]


Global genetic differentiation of complex traits shaped by natural selection in humans

Nat Commun
PMCID: 5951811
PMID: 29760457
DOI: 10.1038/s41467-018-04191-y
call_split See protocol

[…] AF <0.01 and Hardy–Weinberg equilibrium (HWE) P<10-6 were removed from the genotype data for each population, respectively, resulting in 6,160,018 SNPs in common across the three populations. We used GCTA to construct the genetic relationship matrix (GRM) using the SNPs present in HapMap phase 3 project (HapMap3; m = ~1.2 million SNPs) and generate a set of unrelated individuals at a relatedness t […]


Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

BMC Genet
PMCID: 5948690
PMID: 29751743
DOI: 10.1186/s12863-018-0620-0

[…] We developed an analysis approach to run the conditional GWAS analysis, similar to the GCTA-COJO approach in GCTA []. However, GCTA-COJO uses GWAS summary data while we have reanalyzed the data after fitting only the lead SNP(s) on a chromosome. Furthermore, we used imputed dosage data […]


Systematic analysis of copy number variation associated with congenital diaphragmatic hernia

Proc Natl Acad Sci U S A
PMCID: 5960281
PMID: 29712845
DOI: 10.1073/pnas.1714885115

[…] hole-genome data. Concordant SNPs present in both groups were selected using the selectvariant function from GATK () and converted into binary file by Plink (). PCA weights were computed by Plink and GCTA software ().The first 20 principal components from all samples were generated and plotted in an R program () (see for more details). Population control samples were purchased from the Coriell In […]


Genome Wide Association Analysis of Age Dependent Egg Weights in Chickens

Front Genet
PMCID: 5932955
PMID: 29755503
DOI: 10.3389/fgene.2018.00128

[…] .org).We calculated SNP-based heritability (hsnp2) (Lee et al., ) and pairwise genetic correlations of EW traits were using a restricted maximum likelihood (REML) approach implemented in the software GCTA v1.24 (Yang et al., ). This enabled us to estimate the contribution of genome-wide significant SNPs to phenotypic variance based on a genetic matrix constructed from all eligible SNPs. […]


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GCTA institution(s)
Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia

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