DHOEM: a statistical simulation software for simulating new markers in real SNP marker data

BMC Bioinformatics

Software

Laval Jacquin¹  Nourollah Ahmadi¹  Cécile Grenier¹  Tuong-Vi Cao¹ 

[1] CIRAD, UMR AGAP, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Avenue Agropolis, 34398, Montpellier Cedex 5, France;

关键词: Data simulation;    Data structure;    Likelihood;    Non-parametric;    LD;    Haplotypes;    SNP;    Genomic relationship matrix;    Minor allele frequency;   

DOI  :  10.1186/s12859-015-0830-7

 received in 2015-06-22, accepted in 2015-11-16,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundNumerous simulation tools based on specific assumptions have been proposed to simulate populations. Here we present a simulation tool named DHOEM (densification of haplotypes by loess regression and maximum likelihood) which is free from population assumptions and simulates new markers in real SNP marker data. The main objective of DHOEM is to generate a new population, which incorporates real and simulated SNP by statistical learning from an initial population, which match the realized features of the latter.ResultsTo demonstrate DHOEM’s abilities, we used a sample of 704 haplotypes for 12 chromosomes with 8336 SNP from a synthetic population, used for breeding upland rice in Latin America. The distributions of allele frequencies, pairwise SNP LD coefficients and data structures, before and after marker densification of the associated marker data set, were shown to be in relatively good agreement at moderate degrees of marker densification. DHOEM is a user-friendly tool that allows the user to specify the level of marker density desired, with a user defined minor allele frequency (MAF) limit, which is produced in a reasonable computation time.ConclusionsDHOEM is a user-friendly and useful tool for simulation and methodological studies in quantitative genetics and breeding.

【 授权许可】

CC BY   
© Jacquin et al. 2015