Calculating minor allele concordance

Question

[Vivek]

Hi,

I have performed an imputation on genotyped data for around 100k individuals, since we also happen to have exome sequencing for a subset of these people on which I have done variant calling, I wanted to use this as a QC measure to evaluate the accuracy of my imputation.

However when you calculate a direct genotype concordance using PLINK the rare SNPs get a really high concordance rate owing to the fact that a majority of them have the major allele, so I have seen in papers that most people show plots with just the minor allele concordance. I wanted to check how I could go about computing this and if there is some software that can do this out of the box.

Thanks!