I am trying to split whole chromosome haplotypes or haplotypes in long phase blocks on common recombination points to haplotype blocks that can go into downstream analysis.
See also here for information about haplotype blocks.
Are HaploView and Plink still the best tools to do this? HaploView has not been developed/maintained for many years. Plink I never know which version to use, and I am not very familiar with the Plink data formats. And both don't work direct on phased VCF/BCF files.
Is there any recent/maintained tool that can estimate and visualize haplotype blocks, preferable interactively and using phased VCF/BCF as input? And can deal with large VCF/BCF files (in number of samples and variants)?