GSR: Editing - HAP-SAMPLE Simulator

You may request changes to this simulator by navigating to the Basic, Details, and Citations/Applications tabs. When you are finished, open the Submit tab. To return back to the simulator view, click HAP-SAMPLE. Finally, please take note of the GSR simulator privacy policy.
HAP-SAMPLE
An association simulator for candidate regions or genome scans
HAP-SAMPLE is a web application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be "genotyped," along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans. The stand-alone software is also available.
0.12
01-01-2007
01-01-2007
https://sites.google.com/a/umich.edu/leeshawn/software
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
    • 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: 17785348], Wright FA, Huang H, Guan X, Gamiel K, Jeffries C, Barry WT, de Villena FP, Sullivan PF, Wilhelmsen KC, Zou F, Simulating association studies: a data-based resampling method for candidate regions or whole genome scans., Bioinformatics, 10-01-2007, https://www.ncbi.nlm.nih.gov/pubmed/?term=17785348,Primary Citation
      [Pubmed ID: 18285755], Tan HY, Callicott JH, Weinberger DR, Intermediate phenotypes in schizophrenia genetics redux: is it a no brainer?, Mol Psychiatry, 03-01-2008, https://www.ncbi.nlm.nih.gov/pubmed/?term=18285755,, Application
      [Pubmed ID: 19344520], Chai HS, Sicotte H, Bailey KR, Turner ST, Asmann YW, Kocher JP, GLOSSI: a method to assess the association of genetic loci-sets with complex diseases., BMC Bioinformatics, 04-03-2009, https://www.ncbi.nlm.nih.gov/pubmed/?term=19344520,, Application
      [Pubmed ID: 20529910], Zhang X, Huang S, Zou F, Wang W, TEAM: efficient two-locus epistasis tests in human genome-wide association study., Bioinformatics, 06-15-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=20529910,, Application
      [Pubmed ID: 20657396], Aguiar-Pulido V, Seoane JA, Rabuñal JR, Dorado J, Pazos A, Munteanu CR, Machine learning techniques for single nucleotide polymorphism--disease classification models in schizophrenia., Molecules, 07-12-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=20657396,, Application
      [Pubmed ID: 20842628], Chen X, Wang L, Hu B, Guo M, Barnard J, Zhu X, Pathway-based analysis for genome-wide association studies using supervised principal components., Genet Epidemiol, 11-01-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=20842628,, Application
      [Pubmed ID: 21266443], Wang L, Jia P, Wolfinger RD, Chen X, Grayson BL, Aune TM, Zhao Z, An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies., Bioinformatics, 03-01-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=21266443,, Application
      [Pubmed ID: 21611176], Hou L, Phillips C, Azaro M, Brzustowicz LM, Bartlett CW, Validation of a cost-efficient multi-purpose SNP panel for disease based research., PLoS One, 01-01-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=21611176,, Application
      [Pubmed ID: 22257666], Kang CJ, Marjoram P, Exact coalescent simulation of new haplotype data from existing reference haplotypes., Bioinformatics, 03-15-2012, https://www.ncbi.nlm.nih.gov/pubmed/?term=22257666,, Application
      [Pubmed ID: 23161487], Xu Y, Wu Y, Song C, Zhang H, Simulating realistic genomic data with rare variants., Genet Epidemiol, 02-01-2013, https://www.ncbi.nlm.nih.gov/pubmed/?term=23161487,, Application
      [Pubmed ID: 24718920], Nurnberger JI Jr, Koller DL, Jung J, Edenberg HJ, Foroud T, Guella I, Vawter MP, Kelsoe JR, Identification of pathways for bipolar disorder: a meta-analysis., JAMA Psychiatry, 06-01-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24718920,, Application
      [Pubmed ID: 24719383], Huang A, Martin ER, Vance JM, Cai X, Detecting genetic interactions in pathway-based genome-wide association studies., Genet Epidemiol, 05-01-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24719383,, 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).