GCTA pipeline

GCTA specifications

Information


Unique identifier OMICS_04898
Name GCTA
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

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Publication for Genome-wide Complex Trait Analysis

GCTA citations

 (8)
2017
PMCID: 5517526

[…] appendicular lean mass)., to estimate the phenotypic variance explained by the genotyped snps in the framingham heart study (fhs), we used a restricted maximum likelihood model implemented in the gcta (genome-wide complex trait analysis) tool package57, 58 and adjusted for the same set of covariates included in our gwas., finally, we examined associations between all imputed snps in/near five […]

2017
PMCID: 5452641

[…] in our study are also based on release 5. we used gcta 1.02 (yang et al. 2011) to estimate genetic covariance matrix of snps, followed by using reml (restricted maximum likelihood) implemented in gcta to estimate narrow sense heritability (vg/vp). to evaluate the influence of population structures on our observed phenotype, we used the smartpca program of eigensoft 5.0.2 (patterson et al. […]

2017
PMCID: 5580897

[…] lead snp in the conditional analysis. because genome-wide significant snps were also found outside of this range for the lpa gene region, the conditional analysis was extended to a range of 1.76 mb. gcta uses the summary statistics of the meta-analysis plus one reference population for ld calculation. as reference population, a combined genotype dataset of kora f3 and kora f4 was used (n = […]

2017
PMCID: 5386877

[…] genetic-relationship matrices and calculate marker-based additive heritability (h2g) of organohalogen serum levels with a restricted maximum likelihood [reml (yang et al. 2010)] model implemented in gcta software (yang et al. 2011; http://cnsgenomics.com/software/gcta/). the heritability estimation indicates the proportion of the total organohalogen levels (phenotypic variance or vp) accounted […]

2016
PMCID: 4872404

[…] a genetic-relationship matrix and calculate marker-based additive heritability (h2) of log-transformed crp levels after exclusion of outliers. a restricted maximum-likelihood model implemented in gcta software40 was utilized with the same sociodemographic covariates as above, plus 10 genetic ancestry principal components and a covariate indicating child phenotype (asd, dd, gp). […]

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

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