Hi I need to compare genotype calls between two datasets, one has been genotyped the other has been genotyped and imputed; the subjects in both datasets are the same.
I would need to calculate genotype concordance rates only for those subjects that carry a minor allele. Has anyone has any experience in doing this?
I was trying to use plink, with the function "--merge-mode 7" I obtain for which subjects genotypes are different at a specific SNP. Also with plink I can extract with function "--recode-rlist" those subjects at each SNP that carry a minor allele. However I am not sure if there is an efficient way for merging the two pieces of information (I obtain two distinct tables of results in plink and by the way they are formatted it is not so straightforward how to combine them).
Thank you for any suggestion.