Hello dear experts, I have conducted GWAS on a plant data, and identified some candidate genes, which are associated with my trait. Now, I want to find haplotypes of those candidate genes. I know how to do haplotype analysis in haploview to find haplotype blocks. I used haploview to find haploytype blocks in my significant snps, but i am confused about, how to do haplotype analysis of candidate genes. I read a lot of papers to find any way to do haplotype analysis, but couldn't find any clear method. It would be great help, if any expert guides me about it. I have given a paper link to understand, what type of haplotypes I want to find. In this paper, they did haplotype analysis of some candidate genes, and found 5 haplotype i.e. hap 1, hap2, hap3, hap 4 and hap 5. I want an analysis like this and link of paper https://thericejournal.springeropen.com/articles/10.1186/s12284-019-0351-5