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GWAsimulator specifications

Information


Unique identifier OMICS_04166
Name GWAsimulator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for GWAsimulator

GWAsimulator citations

 (6)
library_books

Computational methods using genome wide association studies to predict radiotherapy complications and to identify correlative molecular processes

2017
Sci Rep
PMCID: 5324069
PMID: 28233873
DOI: 10.1038/srep43381

[…] o probe the number of false positive SNPs included in the prediction model, we injected phoney SNPs into the rectal bleeding modeling process. To do this, we generated 60,000 synthetic SNPs using the GWAsimulator (http://biostat.mc.vanderbilt.edu/wiki/Main/GWAsimulator) relying on HapMap CEU data. With a p-value cutoff of 0.001, 74 SNPs remained. We combined these SNPs with 749 SNPs that were orig […]

library_books

r2VIM: A new variable selection method for random forests in genome wide association studies

2016
BioData Min
PMCID: 4736152
PMID: 26839594
DOI: 10.1186/s13040-016-0087-3

[…] nd relatively large effects that depend on the MAF of the corresponding SNPs. Haplotypes from 381 European individuals provided by the 1000 genomes project [] were used as input data for the software GWAsimulator [] to simulate new haplotypes for a case–control study. 554,813 SNPs from the Illumina Human660W chip were selected and 10 replicates generated. We used total sample sizes of 2000 and 600 […]

library_books

Jackknife based gene gene interactiontests for untyped SNPs

2015
BMC Genet
PMCID: 4506584
PMID: 26187382
DOI: 10.1186/s12863-015-0225-9

[…] erated genotype data of the individuals in the general population based on the observed haplotype distributions in 180 kb and 174 kb regions of chromosomes 18 and 21 from the HapMap CEU samples using GWAsimulator [], respectively. Thus, the simulated individuals have genotypes in the regions of chromosomes 18 and 21 with similar LD structure to that of the HapMap CEU samples. We chose a pair of SN […]

library_books

Improving Power of Genome Wide Association Studies with Weighted False Discovery Rate Control and Prioritized Subset Analysis

2012
PLoS One
PMCID: 3322139
PMID: 22496761
DOI: 10.1371/journal.pone.0033716

[…] We used a rapid whole-genome simulation program, the GWAsimulator (http://biostat.mc.vanderbilt.edu/wiki/Main/GWAsimulator), to generate GWAS data sets. The GWAsimulator implements a rapid moving-window algorithm to simulate whole genome case-control […]

library_books

Ranking causal variants and associated regions in genome wide association studies by the support vector machine and random forest

2011
Nucleic Acids Res
PMCID: 3089490
PMID: 21317188
DOI: 10.1093/nar/gkr064

[…] The GWAsimulator program () produces case and control genome-wide SNP genotypes under a logistic regression disease model. It takes as input a control file that specifies various parameters such as relati […]

library_books

Simulating gene environment interactions in complex human diseases

2010
Genome Med
PMCID: 2873799
PMID: 20346093
DOI: 10.1186/gm142

[…] can be simulated directly and only the required number of cases and controls needs to be simulated. This second approach has been used by many simulation programs, such as HapSample [], hapgen [] and GWAsimulator []. As a compromise between these two approaches, a rejection-sampling algorithm can be used to simulate samples without simulating a large population (for example, genomeSIMLA []). This […]

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GWAsimulator institution(s)
Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA

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