GSR: Editing - cosi Simulator

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cosi
A coalescent-based simulator with a demographic model calibrated from empirical data.
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.
1.2.1
10-25-2005
10-08-2010
http://www.broadinstitute.org/~sfs/cosi/

Attribute Tree Control

Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.

Every sub-attribute is selected
Not all sub-attributes are selected
  • Target
    • Type of Simulated Data
      • Genotype at Genetic Markers
      • Diploid DNA Sequence
      • Haploid DNA Sequence
      • RNA
      • Sex Chromosomes
      • Mitochondrial DNA
      • Protein Sequence
      • Sequencing Reads
      • Phenotype
    • Variations
      • Biallelic Marker
      • Multiallelic Marker
      • Single Nucleotide Variation
      • Amino acid variation
      • Microsatellite
      • Insertion and Deletion
      • CNV
      • Inversion and Rearrangement
      • Alternative Splicing
      • Missing Genotypes
      • Genotype or Sequencing Error
      • Other
  • Simulation Method
    • Standard Coalescent
    • Exact Coalescent
    • Machine Learning
    • Forward-time
    • Resample Existing Data
    • Phylogenetic
    • Gene dropping
    • Other
  • Input
    • Data Type
      • Allele Frequencies
      • Empirical
      • Ancestral Sequence
      • Saved simulation
      • Reference genome
      • Other
    • File format
      • Arlequin
      • CREATE
      • Fstat
      • GDA
      • Genepop
      • MIGRATE
      • MS
      • SAM or BAM
      • NEXUS
      • Phylip
      • STRUCTURE
      • XML
      • Tree Sequence
      • Program Specific
      • Other
  • Output
    • Data Type
      • Genotype or Sequence
      • Phenotypic Trait
      • Individual Relationship
      • Demographic
      • Mutation
      • Methylation
      • Gene Expression
      • Protein Expression
      • Linkage Disequilibrium
      • Diversity Measures
      • Fitness
      • Sequencing Reads
        • Illumina
        • Roche 454
        • SOLiD
        • IonTorrent
        • PacBio
        • Nanopore
        • Other
      • Other
    • File Format
      • Arlequin
      • Fasta or Fastq
      • Fstat
      • Genepop
      • Linkage
      • MIGRATE
      • MS
      • PED
      • Phylip
      • NEXUS
      • STRUCTURE
      • VCF
      • SAM or BAM
      • Tree Sequence
      • Program Specific
      • Other
    • Sample Type
      • Random or Independent
      • Sibpairs, Trios and Nuclear Families
      • Extended or Complete Pedigrees
      • Case-control
      • Longitudinal
      • Other
  • Phenotype
    • Trait Type
      • Binary or Qualitative
      • Quantitative
      • Multiple
    • Determinants
      • Single Genetic Marker
      • Multiple Genetic Markers
      • Sex-linked
      • Gene-Gene Interaction
      • Environmental Factors
      • Gene-Environment Interaction
  • Evolutionary Features
    • Demographic
      • Population Size Changes
        • Constant Size
        • Exponential Growth or Decline
        • Logistic Growth
        • Bottleneck
        • Carrying Capacity
        • User Defined
      • Gene Flow
        • Stepping Stone Models
        • Island Models
        • Continent-Island Models
        • Sex or Age-Specific Migration Rates
        • Influenced by Environmental Factors
        • Admixed Population
        • User-defined Matrix
        • Other
      • Spatiality
        • Discrete Models
        • Continuous Models
        • Landscape Factors
    • Life Cycle
      • Discrete Generation Model
      • Age structured
      • Overlapping Generation
      • User-Defined transition matrices
    • Mating System
      • Random Mating
      • Monogamous
      • Polygamous
      • Haplodiploid
      • Selfing
      • Age- or Stage-Specific
      • Assortative or Disassortative
      • Other
    • Fecundity
      • Constant Number
      • Randomly Distributed
      • Individually Determined
      • Influenced by Environment
      • Other
    • Natural Selection
      • Determinant
        • Single-locus
        • Multi-locus
        • Codon-based
        • Fitness of Offspring
        • Phenotypic Trait
        • Environmental Factors
      • Models
        • Directional Selection
        • Balancing Selection
        • Multi-locus models
        • Epistasis
        • Random Fitness Effects
        • Disruptive
        • Phenotype Threshold
        • Frequency-Dependent
        • Other
    • Recombination
      • Uniform
      • Varying Recombination Rates
      • Gene Conversion Allowed
    • Mutation Models
      • Two-allele Mutation Model
      • Markov DNA Evolution Models
      • k-Allele Model
      • Infinite-allele Model
      • Infinite-sites Model
      • Stepwise Mutation Model
      • Codon and Amino Acid Models
      • Indels and Others
      • Heterogeneity among Sites
      • Others
    • Events Allowed
      • Population Merge and Split
      • Varying Demographic Features
      • Population Events
      • Varying Genetic Features
      • Change of Mating Systems
      • Other
    • Other
      • Phenogenetic
      • Polygenic background
  • Interface
    • Command-line
    • Graphical User Interface
    • Integrated Development Environment
    • Script-based
    • Web-based
  • Development
    • Tested Platforms
      • Windows
      • Mac OS X
      • Linux and Unix
      • Solaris
      • Others
    • Language
      • C or C++
      • Java
      • R
      • Python
      • Perl
      • Visual Basic
      • Other
    • License
      • GNU Public License
      • BSD
      • Creative Commons
      • MIT
      • Other
  • GSR Certification
    • Accessibility
    • Documentation
    • Application
    • Support

Summary of Proposed Changes

Step 2: Review list of proposed attribute addition(s) and subtraction(s).

To Add

    To Remove

      Can't Find the Attribute You Are Looking For?

      If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab.

      You may add citations by pmid, add citations by direct entry, remove citations (using the recycling bin icon), and edit citations (using the rarely seen edit icon) that were originally entered by direct entry.

      Summary of Proposed Changes

      To Add

      To Remove

      Current Citations/Applications

      [Pubmed ID: 7152526], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=7152526,, Application
      [Pubmed ID: 16251467], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=16251467,Primary Citation
      [Pubmed ID: 25799106], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=25799106,, Application
      [Pubmed ID: 25809955], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=25809955,, Application
      [Pubmed ID: 25897803], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=25897803,, Application
      [Pubmed ID: 25966809], Lin KH, Zöllner S, Robust and Powerful Affected Sibpair Test for Rare Variant Association., Genet Epidemiol, 07-01-2015, https://www.ncbi.nlm.nih.gov/pubmed/?term=25966809,, Application
      [Pubmed ID: 26282996], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=26282996,, Application
      [Pubmed ID: 26319403], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=26319403,, Application
      [Pubmed ID: 26772743], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=26772743,, Application
      [Pubmed ID: 27341039], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=27341039,, Application
      [Pubmed ID: 27355347], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=27355347,, Application
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      Please inform the GSR team here if you would like to see an attribute added to the attribute tree (or any other changes to the simulator description system as it exists).