The linkage method: a novel approach for SNP detection and haplotype reconstruction from a single diploid individual using next-generation sequence data.

When we sequence a diploid individual, the output actually comprises two genomes: one from the paternal parent and the other from the maternal parent. In this study, we introduce a novel heuristic algorithm for distinguishing single-nucleotide polymorphisms (SNPs) from the two parents and phasing them into haplotypes. The algorithm is unique because it simultaneously performs SNP calling and haplotype phasing. This approach can exploit the linkage information of nearby SNPs, which facilitates the efficient removal of haplotypes that originate from incorrectly mapped short reads. Using simulated data we demonstrated that our approach increased the accuracy of SNP calls. The haplotype reconstruction performance depended largely on the density of SNPs. Using current next-generation sequence technology with a relatively short read length, reasonable performance is expected when this approach is applied to species with an average of five heterozygous sites per 1 kb. The algorithm was implemented as the program "linkSNPs."