In this paper we have focused exclusively on genetic data from human samples but our methods may also be useful in the fields of animal and plant genetics where cohorts with high levels of relatedness are prevalent [49]. This method may also find utility in studies that aim to locate IBD segments between individuals. Based on these results we might suggest that a strategy of estimating haplotypes with SHAPEIT2 followed by application of the GERMLINE method [50] for IBD inference from haplotype data may provide an accurate and efficient solution. As cohorts increase in size, or as cohorts are combined, the chance of any individual sharing a close relative in the cohort increases. Methods such as SHAPEIT2, that can accurately leverage this IBD information when estimating haplotypes may help to extract the most information from such large cohorts.
