CandiHap A haplotype analysis toolkit for natural variation study

Haplotype blocks greatly assist association-based mapping of casual candidate genes by significantly reducing genotyping effort. The gene haplotype, which could be used to evaluate variants of affected traits captured from the gene region. While there is a rising interest in gene haplotypes, much of the corresponding analysis was carried out manually. CandiHap allows rapid and robust haplotype analysis 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 favorable haplotypes of candidate genes for target traits. CandiHap can be run on computers with Windows, Mac, or UNIX platforms in a graphical user interface or command line, and applied to any species, such as plant, animal and microbial. The CandiHap software, user manual, and example datasets are freely available at BioCode: https://ngdc.cncb.ac.cn/biocode/tools/BT007080 or GitHub: https://github.com/xukaili/CandiHap.