GSR: Simulator - GWAsimulator
Attribute | Value |
---|---|
Title | GWAsimulator |
Short Description | A rapid whole genome simulation program |
Long Description | GWAsimulator is a C++ program that can simulate genotype data for SNP chips that are used in genome-wide association (GWA) studies. It implements a rapid moving-window algorithm (Durrant et al. 2004. AJHG 75:35-43) to simulate whole genome case-control or population samples. It also can simulate specific regions if desired. For case-control data, the program retrospectively sample cases and controls according to a user-specified multi-locus disease model. The program requires phased data as input, and the simulated data will have similar LD patterns as the input data. The program can use HapMap phased data as input and has the flexibility of simulating genotypes for different populations and different SNP chips. Because many large-scale GWA data are becoming available, they can be used instead of the HapMap data as the input, as long as the phase information is generated. These data may provide a better representation of the population under study and more accurate LD information than the HapMap due to much larger sample sizes. See the manual for instructions and detailed description of the program |
Version | 2.1 |
Project Started | 2008 |
Last Release | 11 years, 8 months ago |
Homepage | https://biostat.app.vumc.org/wiki/Main/GWAsimulator |
Citations | Li C, Li M, GWAsimulator: a rapid whole-genome simulation program., Bioinformatics, 01-01-2008 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 10-03-2019 (1633 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Genotype at Genetic Markers, |
Variations | Single Nucleotide Variation, |
Simulation Method | Other, |
Input | |
Data Type | Empirical (Hapmap data), |
File format | |
Output | |
Data Type | Genotype or Sequence, |
Sequencing Reads | |
File Format | Program Specific, |
Sample Type | Case-control, |
Phenotype | |
Trait Type | Binary or Qualitative, |
Determinants | Single Genetic Marker, Multiple Genetic Markers, Gene-Gene Interaction, |
Evolutionary Features | |
Demographic | |
Population Size Changes | |
Gene Flow | |
Spatiality | |
Life Cycle | |
Mating System | |
Fecundity | |
Natural Selection | |
Determinant | |
Models | |
Recombination | |
Mutation Models | |
Events Allowed | |
Other | |
Interface | Command-line, |
Development | |
Tested Platforms | Windows, Linux and Unix, |
Language | C or C++, |
License | GNU Public License, |
GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used GWAsimulator.
2019
Fang G, Wang W, Paunic V, Heydari H, Costanzo M, Liu X, Liu X, VanderSluis B, Oately B, Steinbach M, et al., Discovering genetic interactions bridging pathways in genome-wide association studies., Nat Commun, 09-19-2019 [Abstract]
Zhang S, Jiang W, Ma RC, Yu W, Region-based interaction detection in genome-wide case-control studies., BMC Med Genomics, 12-30-2019 [Abstract]