I have genotype data (Illumina Global Screening Array) from ~700 individuals.
I am also genotyping 1 SNP in using the TaqMan assay, and I need to check the concordance between the chip genotypes and the TaqMan genotypes for all individuals in my sample.
To do this, I need to extract the genotype for all individuals at 1 specific SNP that is genotyped on this array. The data are currently stored in a PLINK bed file. All suggestions are welcome.