ArticleMolecular genetics and genomics : MGG2017
AntCaller: an accurate variant caller incorporating ancient DNA damage.
Article in Molecular genetics and genomics : MGG, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Lessons learned: Recommendations for reproducible paleogenomic data analyses.American journal of human genetics · 2025Review
- A method to generate capture baits for targeted sequencing.Nucleic acids research · 2023Article
- HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph.PLoS computational biology · 2023Article
- Article
- Pangenome Graphs.Annual review of genomics and human genetics · 2020Review
- The presence and impact of reference bias on population genomic studies of prehistoric human populations.PLoS genetics · 2019Article
- snpAD: an ancient DNA genotype caller.Bioinformatics (Oxford, England) · 2018Article
- ARIADNA: machine learning method for ancient DNA variant discovery.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
Corrections and comments
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Authors and funding
6 authors.
Funding
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Abstract
Ancient DNA obtained from ancient samples, such as sediments, bones, and teeth, is an important genetic resource that can be used to reconstruct an evolutional history of humans, animals, and plants. The application of high-throughput sequencing enables the research of ancient DNA to be conducted in a whole genome scale. However, post-mortem DNA damage mainly caused by deamination of cytosine to uracil (or methylated cytosine to thymine) may confound the variant calling and downstream analysis. In this article, we develop a Python program to implement a new variant caller, "AntCaller", which extracts the information on nucleotide substitutions from sequencing data and calculates the probability of each genotype based on a Bayesian rule. Through both simulation studies and real data analyses, it was shown that our method reduced the false discovery rate caused by nucleotide misincorporations and outperformed two mainstream variant callers (i.e., GATK and SAMtools) in terms of calling accuracy. In a real application with serious DNA damage, AntCaller still outperformed GATK and SAMtools combined with quality score recalling.
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Registered trials
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