Although genotype concordance analysis experiments using different sequencing and genotyping platforms have been performed previously [2, 8], no reports on attempts to explain the observed differences were made. Here we tried to scrutinize the underlying genotyping process proxy such as genotyping quality metrics to find a possible explanation for the discordance pattern. Unfortunately, the genotyping discordance of the observed levels (less than 1%) is usually an underestimation, and does not motivate investigations into the nature of the discordant genotype calling. However, we show that discordant genotypes tend to form clusters in a 2-dimensional space, where the most vivid dimensions are the genotyping quality and technical metrics obtained from the BeadChip genotyping pipeline. Therefore, speculation on possibly lower precision of the BeadChip genotyping platform, as compared to WGS-based pipelines, might find a new conceivable basis upon further investigation. Genotype assignment in the array pipelines is based on marker clustering in a 2-dimensional space (clusters A/A, A/B, B/B), which might happen to be erroneous due to poor cluster separation. This clusterization problem may possibly be solved by incorporating additional dimensions into the
