Hi all, I am trying to do imputation for my data with HapMap reference using MACH. But I am confused with .legend and .phased file of those. I have hapmap .legend file but it is different for each chromosome and .phased file I am not able to find.
Can anybody guide me for selection of .phased and .legend files. Should I split my .ped file and go ahead or I can do it with entire file (file contains 90patients and ~45000 markers)??
Thanks in advance for guidance.