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GSR: Simulator - HAP-SAMPLE
| Attribute | Value |
|---|---|
| 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 | 18 years, 3 months ago |
| Homepage | https://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, Oct. 1, 2007 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | Feb. 8, 2018 (2589 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence |
| Variations | Biallelic Marker, Single Nucleotide Variation |
| Simulation Method | Resample Existing Data |
| Input | |
| Data Type | Empirical (Hapmap data) |
| File format | |
| Output | |
| Data Type | Genotype or Sequence |
| Sequencing Reads | |
| File Format | Program Specific |
| Sample Type | Sibpairs, Trios and Nuclear Families, Case-control |
| Phenotype | |
| Trait Type | Binary or Qualitative |
| Determinants | Single 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 | |
| Interface | Command-line, Web-based |
| Development | |
| Tested Platforms | Linux and Unix |
| Language | C or C++ |
| License | GNU Public License |
| GSR Certification | Documentation, Support |
Number of Primary Citations: 1
Number of Non-Primary Citations: 11
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, June 1, 2014 [Abstract]
Huang A, Martin ER, Vance JM, Cai X, Detecting genetic interactions in pathway-based genome-wide association studies., Genet Epidemiol, May 1, 2014 [Abstract]
2013
Xu Y, Wu Y, Song C, Zhang H, Simulating realistic genomic data with rare variants., Genet Epidemiol, Feb. 1, 2013 [Abstract]
2012
Kang CJ, Marjoram P, Exact coalescent simulation of new haplotype data from existing reference haplotypes., Bioinformatics, March 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, March 1, 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, Jan. 1, 2011 [Abstract]
2010
Zhang X, Huang S, Zou F, Wang W, TEAM: efficient two-locus epistasis tests in human genome-wide association study., Bioinformatics, June 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, July 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, Nov. 1, 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, April 3, 2009 [Abstract]
2008
Tan HY, Callicott JH, Weinberger DR, Intermediate phenotypes in schizophrenia genetics redux: is it a no brainer?, Mol Psychiatry, March 1, 2008 [Abstract]