Illumina Omni2.5 genotyping get actual genotypes.
0
0
Entering edit mode
4 months ago
nhaus ▴ 100

Hello,

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. GType, 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.

Cheers!

genotyping omni illumina • 94 views
ADD COMMENT

Login before adding your answer.

Traffic: 1116 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6