GSR: Simulator - GCTA

Basic Package Attributes
AttributeValue
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 6 years, 7 months ago
Homepagehttp://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
Documentation
Application
Support

Last evaluated05-16-2019 (520 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated Data
VariationsOther,
Simulation MethodResample Existing Data,
Input
Data TypeOther,
File formatOther,
Output
Data TypePhenotypic Trait,
Sequencing Reads
File FormatOther,
Sample Type
Phenotype
Trait TypeBinary or Qualitative, Quantitative, Multiple,
DeterminantsMultiple 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
OtherPolygenic background,
InterfaceCommand-line,
Development
Tested PlatformsLinux and Unix,
LanguageC or C++,
LicenseGNU Public License, Other,
GSR CertificationAccessibility, Documentation, Support,

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