GSR: Editing - GASP Simulator

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GASP
Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models.
The Genometric Analysis Simulation Program (G.A.S.P.) is a software tool that can generate samples of family data based on user specified genetic models. Data generated can be as simple as a single sample of random individuals with a single normally distributed trait or as complex as thousands of samples of extended families with multiple traits based on a linear combination of major locus, polygenic, common sibship environment and covariate components. Traits can be generated based on a number of user specified components, and components can be unique to a single trait or shared by multiple traits. The user first specifies a list of all desired components and then creates each trait by specifying the desired component weighted by its contribution to the phenotypic variance. G.A.S.P. can be used in two ways. First, data can be generated in a standalone fashion. The resulting family data can be saved and then used as sample data for demonstrating applications and methods of genetic analysis or for testing and verifying newly developed algorithms in statistical genetics. A simple driver ("dataonly") is provided for this application. Second, data can be generated and analyzed immediately using an existing statistical package. A driver can be designed to call subroutine versions of widely available genetic analysis programs.
V3.33 (7/30/2003)
10-24-1997
07-30-2003
http://research.nhgri.nih.gov/gasp/
None

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

      Wilson, A.F., Bailey-Wilson, J.E., Pugh, E.W., Sorant, A.J.M., The Genometric Analysis Simulation Program (G.A.S.P.): a software tool for testing and investigating methods in statistical genetics, Am J Hum Genet., , Primary Citation
      [Pubmed ID: 2753353], Amos CI, Elston RC, Wilson AF, Bailey-Wilson JE, A more powerful robust sib-pair test of linkage for quantitative traits., Genet Epidemiol, 01-01-1989, https://www.ncbi.nlm.nih.gov/pubmed/?term=2753353,, Application
      [Pubmed ID: 7607415], Nick TG, George V, Elston RC, Wilson AF, Statistical validity for testing associations between genetic markers and quantitative traits in family data., Genet Epidemiol, 01-01-1995, https://www.ncbi.nlm.nih.gov/pubmed/?term=7607415,, Application
      [Pubmed ID: 8314066], Wilson AF, Elston RC, Statistical validity of the Haseman-Elston sib-pair test in small samples., Genet Epidemiol, 01-01-1993, https://www.ncbi.nlm.nih.gov/pubmed/?term=8314066,, Application
      [Pubmed ID: 10762546], Wilson AF, Sorant AJ, Equivalence of single- and multilocus markers: power to detect linkage with composite markers derived from biallelic loci., Am J Hum Genet, 05-01-2000, https://www.ncbi.nlm.nih.gov/pubmed/?term=10762546,, Application
      [Pubmed ID: 16618369], Mandal DM, Sorant AJ, Atwood LD, Wilson AF, Bailey-Wilson JE, Allele frequency misspecification: effect on power and Type I error of model-dependent linkage analysis of quantitative traits under random ascertainment., BMC Genet, 04-20-2006, https://www.ncbi.nlm.nih.gov/pubmed/?term=16618369,, Application
      [Pubmed ID: 16736037], Doan BQ, Sorant AJ, Frangakis CE, Bailey-Wilson JE, Shugart YY, Covariate-based linkage analysis: application of a propensity score as the single covariate consistently improves power to detect linkage., Eur J Hum Genet, 09-01-2006, https://www.ncbi.nlm.nih.gov/pubmed/?term=16736037,, Application
      [Pubmed ID: 16909384], Gillanders EM, Pearson JV, Sorant AJ, Trent JM, O'Connell JR, Bailey-Wilson JE, The value of molecular haplotypes in a family-based linkage study., Am J Hum Genet, 09-01-2006, https://www.ncbi.nlm.nih.gov/pubmed/?term=16909384,, 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).