A new generation of high-throughput sequencing strategies will soon lead to the acquisition of high-coverage genomic profiles of hundreds to thousands of individuals within species, generating unprecedented levels of information on the frequencies of nucleotides segregating at individual sites. However, because these new technologies are error prone and yield uneven coverage of alleles in diploid individuals, they also introduce the need for novel methods for analyzing the raw read data. A maximum-likelihood method for the estimation of allele frequencies is developed, eliminating both the need to arbitrarily discard individuals with low coverage and the requirement for an extrinsic measure of the sequence error rate. The resultant estimates are nearly unbiased with asymptotically minimal sampling variance, thereby defining the limits to our ability to estimate population-genetic parameters and providing a logical basis for the optimal design of population-genomic surveys
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