I would like to hear your advice on/recommendation of a tools of estimating Linkage Disequilibrium/Recombination Rate and RR hot-spot based on NGS population data.
For me, I have gotten known with LDhat. But, I have implemented in my study. I wonder if there are robust but more easy-for-use tools like LDhat. Also, I would like to hear your experience of using those ones or good guides for them.
Thanks in advance.