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Literature DB >> 16188927

HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients.

Abstract

UNLABELLED: We have developed a simulation tool HapSim for the generation of haplotype data. The simulated haplotypes are such that their allele frequencies and linkage disequilibrium coefficients match exactly those estimated in a real sample. AVAILABILITY: The program is available as an R package and can be downloaded from http://cran.r-project.org/.

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Year: 2005 PMID： 16188927 DOI： 10.1093/bioinformatics/bti689

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

30 in total

1. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets.

Authors: Miao-Xin Li; Juilian M Y Yeung; Stacey S Cherny; Pak C Sham
Journal: Hum Genet Date: 2011-12-06 Impact factor: 4.132

2. Power of family-based association designs to detect rare variants in large pedigrees using imputed genotypes.

Authors: Mohamad Saad; Ellen M Wijsman
Journal: Genet Epidemiol Date: 2013-11-15 Impact factor: 2.135

3. GATES: a rapid and powerful gene-based association test using extended Simes procedure.

Authors: Miao-Xin Li; Hong-Sheng Gui; Johnny S H Kwan; Pak C Sham
Journal: Am J Hum Genet Date: 2011-03-11 Impact factor: 11.025

4. Shrinkage estimation of the genomic relationship matrix can improve genomic estimated breeding values in the training set.

Authors: Dominik Müller; Frank Technow; Albrecht E Melchinger
Journal: Theor Appl Genet Date: 2015-03-04 Impact factor: 5.699

5. ARIEL and AMELIA: testing for an accumulation of rare variants using next-generation sequencing data.

Authors: Jennifer L Asimit; Aaron G Day-Williams; Andrew P Morris; Eleftheria Zeggini
Journal: Hum Hered Date: 2012-03-22 Impact factor: 0.444

6. HYST: a hybrid set-based test for genome-wide association studies, with application to protein-protein interaction-based association analysis.

Authors: Miao-Xin Li; Johnny S H Kwan; Pak C Sham
Journal: Am J Hum Genet Date: 2012-09-07 Impact factor: 11.025

HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients.

1. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets.

2. Power of family-based association designs to detect rare variants in large pedigrees using imputed genotypes.

3. GATES: a rapid and powerful gene-based association test using extended Simes procedure.

4. Shrinkage estimation of the genomic relationship matrix can improve genomic estimated breeding values in the training set.

5. ARIEL and AMELIA: testing for an accumulation of rare variants using next-generation sequencing data.

6. HYST: a hybrid set-based test for genome-wide association studies, with application to protein-protein interaction-based association analysis.

7. Identification of key ancestors of modern germplasm in a breeding program of maize.

8. The role of linkage disequilibrium in case-only studies of gene-environment interactions.

9. Sequence kernel association test for quantitative traits in family samples.

10. Modeling X Chromosome Data Using Random Forests: Conquering Sex Bias.