ArticleBioinformatics (Oxford, England)2018
snpAD: an ancient DNA genotype caller.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Western Hunter-Gatherer genetic ancestry contributes to human longevity in the Italian population.GeroScience · 2026Article
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- A global map for introgressed structural variation and selection in humans.Science (New York, N.Y.) · 2026Article
- Enhancement of hidden Markov model analyses for improved inference of archaic introgression in modern humans.Molecular biology and evolution · 2026Article
- A high-coverage Neandertal genome from the Altai Mountains reveals population structure among Neandertals.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Lessons learned: Recommendations for reproducible paleogenomic data analyses.American journal of human genetics · 2025Review
- Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery.Molecular ecology · 2025Article
- Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias.G3 (Bethesda, Md.) · 2025Article
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- Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data.Genome biology · 2025Article
- Resolving the source of branch length variation in the Y chromosome phylogeny.Genome biology · 2025Article
- Whole genomes from the extinct Xerces Blue butterfly can help identify declining insect species.eLife · 2024Article
- Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region.Genome biology and evolution · 2024Article
- Neandertal ancestry through time: Insights from genomes of ancient and present-day humans.bioRxiv : the preprint server for biology · 2024Article
- The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes.Scientific data · 2024Article
- Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics.iScience · 2023Review
- Deep-time paleogenomics and the limits of DNA survival.Science (New York, N.Y.) · 2023Review
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1 author.
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No grant is acknowledged in the PubMed record.
Abstract
Motivation: The 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. Results: I describe an iterative method 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. Availability and implementation: The C++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/. Supplementary information: Supplementary data are available at Bioinformatics online.
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