I think you underestimate the quality and power of short read sequencing. Most well-designed sequence-based genotyping assays take into account the length of th

I think you underestimate the quality and power of short read sequencing. Most well-designed sequence-based genotyping assays take into account the length of the read and are easy to read out. (You are thinking of issues with copy number variation and perhaps assembly of longer genes, which do have issues). The sticky part is the analysis--how realiable are your databases and your algorithm for representing the mix of SNPs and INDELs as %European...that is the question.