More than 110,000 rare markers (MAF < 0.01 in UK Biobank) were included on the two arrays used for the UK Biobank cohort2. Variants occurring at very low frequencies present a particular challenge for genotype calling using array technology. It can be challenging to distinguish a sample that genuinely has the minor allele, from one in which the intensities are in the tails of the distribution of those in the major homozygote cluster (Extended Data Fig. 2). A larger fraction of rare markers fail quality control tests compared to low frequency and common markers, but 84% still pass in all batches (Fig. 2b). We recommend researchers visually inspect cluster plots, similar to Supplementary Fig. 2, for markers of interest using a utility such as Evoker (https://github.com/wtsi-medical-genomics/evoker), especially for rare markers.
