snpAD: An ancient DNA genotype caller

MotivationThe study of ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling.\n\nResultsI describe an expectation-maximization algorithm that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals.\n\nAvailabilityThe C++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/\n\nContactpruefer@eva.mpg.de\n\nSupplementary informationSupplementary data are available at Bioinformatics online.