I am new to GWAS and would appreciate if anyone could help me with my question!
I have an imputed GEN format genotype data. Besides using SNPtest, I am also interested to run the association analysis in R. So, I want to convert the GEN format to a SNPs by sample (individuals) matrix. My question is as follows,
In GEN file each SNP is represented by 3 genotypes (AA, AB or BB) with respective probabilities. Now, in the matrix that I want, I just want the genotype of SNP for each individual. Picking the genotype based on the highest probability is very straightforward. However, if I pick the genotype based on some threshold (for example 0.9) and some SNPs fail to reach the threshold, what to I do in that situation?
I hope my question makes sense! If not I will try to make it clearer1