Hello all,

I am new to this whole realm of PLINK and SNP Arrays. I have got 3 plink datasets all .ped, .map, and .fam files. I want to merge them to do a population genetic diversity analysis. One dataset is Goat 70K SNP array by Illumina. The remaining two are 50K arrays of goat genome.

My questions are

Is it ok to merge datasets from different arrays? How can I merge them (first I thought of just extracting all the common SNPs from 3 datasets and then concatenating them and sorting by chromosome number) Is there any kind of possible problems that can arise from merging and have to be addressed after merging datasets during the analysis? What are the analyses I need to perform for the population genetics study? ( I have been through some papers but all of them do different analyses.)