2604.00837 Genotype-level uncertainty and population-level bias in low-coverage imputation: an empirical framework for non-model organisms
Genotype imputation from low-coverage sequencing (lcWGS) is routine, but the calibration of its uncertainty estimates remains under-investigated in non-model species. We used 36 baboons at 1x coverage to evaluate how population-level quality control (QC) impacts imputation accuracy and the site frequency spectrum (SFS).