GSR: Simulator - cosi

Basic Package Attributes
AttributeValue
Title cosi
Short Description A coalescent-based simulator with a demographic model calibrated from empirical data.
Long Description Population genetic models play an important role in human genetic research, connecting empirical observations about sequence variation with hypotheses about underlying historical and biological causes. More specifically, models are used to compare empirical measures of sequence variation, linkage disequilibrium (LD), and selection to expectations under a "null" distribution. In the absence of detailed information about human demographic history, and about variation in mutation and recombination rates, simulations have of necessity used arbitrary models, usually simple ones. With the advent of large empirical data sets, it is now possible to calibrate population genetic models with genome-wide data, permitting for the first time the generation of data that are consistent with empirical data across a wide range of characteristics. We present here the first such calibrated model and show that, while still arbitrary, it successfully generates simulated data (for three populations) that closely resemble empirical data in allele frequency, linkage disequilibrium, and population differentiation. No assertion is made about the accuracy of the proposed historical and recombination model, but its ability to generate realistic data meets a long-standing need among geneticists. We anticipate that this model, for which software is publicly available, and others like it will have numerous applications in empirical studies of human genetics.
Version 1.2.1
Project Started 2005
Last Release 10 years ago
Homepagehttp://www.broadinstitute.org/~sfs/cosi/
Citations Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D, Calibrating a coalescent simulation of human genome sequence variation., Genome Res, 11-01-2005 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated08-30-2016 (1509 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsBiallelic Marker,
Simulation MethodStandard Coalescent,
Input
Data TypeEmpirical,
File formatProgram Specific,
Output
Data TypeGenotype or Sequence,
Sequencing ReadsOther (Program specified format),
File Format
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline,
Gene FlowUser-defined Matrix,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationVarying Recombination Rates,
Mutation ModelsTwo-allele Mutation Model,
Events AllowedPopulation Merge and Split, Varying Demographic Features,
Other
InterfaceCommand-line, Script-based,
Development
Tested PlatformsMac OS X, Linux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application,

The following 10 publications are selected examples of applications that used cosi.

2016

Chang LC, Li B, Fang Z, Vrieze S, McGue M, Iacono WG, Tseng GC, Chen W, A computational method for genotype calling in family-based sequencing data., BMC Bioinformatics, 01-16-2016 [Abstract]

Lin WY, Liang YC, Conditioning adaptive combination of P-values method to analyze case-parent trios with or without population controls., Sci Rep, 06-24-2016 [Abstract]

Jeng XJ, Daye ZJ, Lu W, Tzeng JY, Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level., PLoS Comput Biol, 06-01-2016 [Abstract]

2015

Epstein MP, Duncan R, Ware EB, Jhun MA, Bielak LF, Zhao W, Smith JA, Peyser PA, Kardia SL, Satten GA, A statistical approach for rare-variant association testing in affected sibships., Am J Hum Genet, 04-02-2015 [Abstract]

Wang Y, Liu A, Mills JL, Boehnke M, Wilson AF, Bailey-Wilson JE, Xiong M, Wu CO, Fan R, Pleiotropy analysis of quantitative traits at gene level by multivariate functional linear models., Genet Epidemiol, 05-01-2015 [Abstract]

Zeng P, Zhao Y, Li H, Wang T, Chen F, Permutation-based variance component test in generalized linear mixed model with application to multilocus genetic association study., BMC Med Res Methodol, 04-22-2015 [Abstract]

Lin KH, Zöllner S, Robust and Powerful Affected Sibpair Test for Rare Variant Association., Genet Epidemiol, 07-01-2015 [Abstract]

Wu B, Pankow JS, Guan W, Sequence Kernel Association Analysis of Rare Variant Set Based on the Marginal Regression Model for Binary Traits., Genet Epidemiol, 09-01-2015 [Abstract]

Pontremoli C, Mozzi A, Forni D, Cagliani R, Pozzoli U, Menozzi G, Vertemara J, Bresolin N, Clerici M, Sironi M, Natural Selection at the Brush-Border: Adaptations to Carbohydrate Diets in Humans and Other Mammals., Genome Biol Evol, 08-28-2015 [Abstract]

1982

García M, Estrada M, Gutiérrez A, Ballester A, González R, Glyoxalase i polymorphism and racial admixture in the Cuban population., Hum Genet, 01-01-1982 [Abstract]


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