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 | 17 years, 2 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, 10-01-2007 [ Abstract, cited in PMC ] |
GSR Certification | Accessibility |
Last evaluated | 02-08-2018 (2234 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, 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]