Abstract: In one method embodiment low-coverage genome sequence data for each individual in a group of related individuals is obtained, the alignment of read sequences is determined relative to a reference sequence and to each other in a padded multiple alignment, the relative likelihoods of the observed base calls and quality scores obtained from the set of sequence reads for each individual for each position are determined for possible individual genotypes at that position, the most likely shared genotype between individuals for each position is determined to define a multi-individual consensus for each position, and individual genotypes and confidence levels are imputed to produce an error-corrected genome sequence for each individual.