CandiHap: a haplotype analysis toolkit for natural variation study

Abstract Haplotype blocks greatly assist association-based mapping of casual candidate genes by significantly reducing the genotyping effort. The gene haplotype, which could be adopted to evaluate the variants of the affected traits captured from the gene region. While there is a rising interest in gene haplotypes, much of the corresponding analyses were carried out manually. CandiHap allows fast and robust haplotype analyses and candidate identification preselection of candidate causal SNPs and InDels from Sanger or next-generation sequencing data. Investigators can use CandiHap to specify a gene or linkage sites based on GWAS and explore favourable haplotypes of candidate genes for target traits. CandiHap can be run on computers with Windows, Mac, or UNIX platforms in graphical user interface or command lines, and applied to any species of plant, animal and microbial. The CandiHap software, user manual, and example datasets are freely available at GitHub: https://github.com/xukaili/CandiHap.