I am currently trying to analyze the results from a genotyping chip (Infinium Omni2.5). The file that I received confuses me however. The structure of the file is something like this.
I have one row per SNP and for each of my analyzed samples there are several columns. I am primarily interested in the genotype (e.g. G/T) at a certain SNP (e.g. chr3, pos 4501234). For each of my samples, there are several columns, which describe the genotype, i.e.
Top Alleles or
Plus/Minus Alleles. My question is, which column I should use if I am only interested in what genotype (i.e. what nucleotides and not BB) my patient has at a given position. I would also by very thankful, if somebody could explain to me what the difference is between these 3 columns, as they all seem to describe something very similar.