recently, I want to do some study on LD relationship of SNPs on whole-genome scale.
i am told that one can use hapmap LD data offerred via hapmap or can use some softwares to simulate.
i: i download the latest LD data and use some data from a publised paper for comparison but found differently not the same.
so i asked the author which data they used and which method they handled. The author told me that the hapmap II+III rel27 b36 version data were get from hapmap which i had download it again, and the software is plink.
while i took some time to look at the software and i realize the different input file format must be convert into.
So, i came across the problem how can i use the original fwd.txt to obtain the plink ped and map file?
ps: although the hapmap offerred us hapmap phase3 r2 plink data, but i just want to learn that how can i handle this problem!
hope that who can give me the answer or softwares or scipts!
and at last, i want to know if there are any significant difference between hapmap data and 1000Gonome project data for LD calculation?