Extended Data Fig. 1: Pipeline to simulate IBD segment data.
From: Accurate detection of identity-by-descent segments in human ancient DNA
We visualize our steps to simulate IBD segment data (see detailed description in Supplementary Note 2). Starting from TSI (Tuscany) high-quality reference haplotypes in the 1000 Genome panel (A), we created haplotype mosaics (B) as any long IBD segment is removed from those. We then copied over IBD segments of the target length (C). We grouped two mosaic haplotypes to obtain diploid individuals but to simplify visualization here we do not depict the second haplotype per individual. (D): To create data typical for imputed low-coverage aDNA, we matched each genotype to a random matching genotype in a panel of aDNA diploid genotypes called from high-coverage aDNA (either 1240k or WGS aDNA data). We then downsampled the high-coverage aDNA panel to the target coverage, imputed genotype probabilities and copied those back to each match.
