GSR: Simulator - HAP-SAMPLE

Basic Package Attributes
AttributeValue
Title HAP-SAMPLE
Short Description An association simulator for candidate regions or genome scans
Long Description 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.
Version 0.12
Project Started 2007
Last Release 13 years, 9 months ago
Homepagehttps://sites.google.com/a/umich.edu/leeshawn/software
Citations 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 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated02-08-2018 (982 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers, Diploid DNA Sequence,
VariationsBiallelic Marker, Single Nucleotide Variation,
Simulation MethodResample Existing Data,
Input
Data TypeEmpirical (Hapmap data),
File format
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatProgram Specific,
Sample TypeSibpairs, Trios and Nuclear Families, Case-control,
Phenotype
Trait TypeBinary or Qualitative,
DeterminantsSingle Genetic Marker, Multiple Genetic Markers,
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation Models
Events Allowed
Other
InterfaceCommand-line, Web-based,
Development
Tested PlatformsLinux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationDocumentation, Support,

The following 11 publications are selected examples of applications that used HAP-SAMPLE.

2014

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 [Abstract]

Huang A, Martin ER, Vance JM, Cai X, Detecting genetic interactions in pathway-based genome-wide association studies., Genet Epidemiol, 05-01-2014 [Abstract]

2013

Xu Y, Wu Y, Song C, Zhang H, Simulating realistic genomic data with rare variants., Genet Epidemiol, 02-01-2013 [Abstract]

2012

Kang CJ, Marjoram P, Exact coalescent simulation of new haplotype data from existing reference haplotypes., Bioinformatics, 03-15-2012 [Abstract]

2011

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 [Abstract]

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 [Abstract]

2010

Zhang X, Huang S, Zou F, Wang W, TEAM: efficient two-locus epistasis tests in human genome-wide association study., Bioinformatics, 06-15-2010 [Abstract]

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 [Abstract]

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 [Abstract]

2009

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 [Abstract]

2008

Tan HY, Callicott JH, Weinberger DR, Intermediate phenotypes in schizophrenia genetics redux: is it a no brainer?, Mol Psychiatry, 03-01-2008 [Abstract]


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