GSR: Simulator - GCTA
Attribute | Value |
---|---|
Title | GCTA |
Short Description | Genome-wide Complex Trait Analysis |
Long Description | 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: 1) Estimate the genetic relationship from genome-wide SNPs; 2) Estimate the inbreeding coefficient from genome-wide SNPs; 3) Estimate the variance explained by all the autosomal SNPs; 3) Partition the genetic variance onto individual chromosomes; 4) Estimate the genetic variance associated with the X-chromosome; 5) Test the effect of dosage compensation on genetic variance on the X-chromosome; 6) Predict the genome-wide additive genetic effects for individual subjects and for individual SNPs; 7) Estimate the LD structure encompassing a list of target SNPs; 8) Simulate GWAS data based upon the observed genotype data; 9) Convert Illumina raw genotype data into PLINK format; 10) Conditional & joint analysis of GWAS summary statistics without individual level genotype data; 11) Estimating the genetic correlation between two traits (diseases) using SNP data; 12) Mixed linear model association analysis |
Version | 1.24 |
Project Started | 2011 |
Last Release | 10 years ago |
Homepage | http://cnsgenomics.com/software/gcta/ |
Citations | Yang J, Lee SH, Goddard ME, Visscher PM, GCTA: a tool for genome-wide complex trait analysis., Am J Hum Genet, 01-07-2011 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 05-16-2019 (1772 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | |
Variations | Other, |
Simulation Method | Resample Existing Data, |
Input | |
Data Type | Other, |
File format | Other, |
Output | |
Data Type | Phenotypic Trait, |
Sequencing Reads | |
File Format | Other, |
Sample Type | |
Phenotype | |
Trait Type | Binary or Qualitative, Quantitative, Multiple, |
Determinants | Multiple Genetic Markers, |
Evolutionary Features | |
Demographic | |
Population Size Changes | |
Gene Flow | |
Spatiality | |
Life Cycle | |
Mating System | |
Fecundity | |
Natural Selection | |
Determinant | |
Models | |
Recombination | |
Mutation Models | |
Events Allowed | |
Other | Polygenic background, |
Interface | Command-line, |
Development | |
Tested Platforms | Linux and Unix, |
Language | C or C++, |
License | GNU Public License, Other, |
GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used GCTA.
2023
He Z, Liu R, Wang M, Wang Q, Zheng J, Ding J, Wen J, Fahey AG, Zhao G, Combined effect of microbially derived cecal SCFA and host genetics on feed efficiency in broiler chickens., Microbiome, 09-01-2023 [Abstract]
Xie L, Qin J, Rao L, Cui D, Tang X, Chen L, Xiao S, Zhang Z, Huang L, Genetic dissection and genomic prediction for pork cuts and carcass morphology traits in pig., J Anim Sci Biotechnol, 09-03-2023 [Abstract]