BRM: a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing.

MOTIVATION: Bulked segregant analysis by deep sequencing (BSA-seq) has been widely used for quantitative trait locus (QTL) mapping in recent years. A number of different statistical methods for BSA-seq have been proposed. However, determination of significance threshold, the key point for QTL identification, remains to be a problem that has not been well solved due to the difficulty of multiple testing correction. In addition, estimation of the confidence interval is also a problem to be solved. RESULTS: In this paper, we propose a new statistical method for BSA-seq, named Block Regression Mapping (BRM). BRM is robust to sequencing noise and is applicable to the case of low sequencing depth. Significance threshold can be reasonably determined by taking multiple testing correction into account. Meanwhile, the confidence interval of QTL position can also be estimated. AVAILABILITY AND IMPLEMENTATION: The R scripts of our method are open source under GPLv3 license at https://github.com/huanglikun/BRM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.