ArticleBMC genomics2015
Impacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Unified Multi-Caller Ensemble (UME) Generates an Unbiased Maize Haplotype Map for Variable Coverage Whole Genome Data.Molecular ecology resources · 2026Article
- Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome.Genome biology · 2026Article
- Artificial intelligence in variant calling: a review.Frontiers in bioinformatics · 2025Review
- Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA.Scientific reports · 2024Article
- Achieving improved accuracy for imputation of ancient DNA.Bioinformatics (Oxford, England) · 2023Article
- An empirical evaluation of genotype imputation of ancient DNA.G3 (Bethesda, Md.) · 2022Article
- Retrospective genomics highlights changes in genetic composition of tiger sharks (Galeocerdo cuvier) and potential loss of a south-eastern Australia population.Scientific reports · 2022Article
- Imputation of Ancient Whole GenomeFrontiers in genetics · 2022Article
- Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA.Ecology and evolution · 2020Article
- ARIADNA: machine learning method for ancient DNA variant discovery.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes.Scientific reports · 2017Article
- AntCaller: an accurate variant caller incorporating ancient DNA damage.Molecular genetics and genomics : MGG · 2017Article
- Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus).Scientific reports · 2017Article
- Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.Genome biology · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMassively parallel sequencing platforms, featuring high throughput and relatively short read lengths, are well suited to ancient DNA (aDNA) studies. Variant identification from short-read alignment could be hindered, however, by low DNA concentrations common to historic samples, which constrain sequencing depths, and post-mortem DNA damage patterns.
resultsWe simulated pairs of sequences to act as reference and sample genomes at varied GC contents and divergence levels. Short-read sequence pools were generated from sample sequences, and subjected to varying levels of "post-mortem" damage by adjusting levels of fragmentation and fragmentation biases, transition rates at sequence ends, and sequencing depths. Mapping of sample read pools to reference sequences revealed several trends, including decreased alignment success with increased read length and decreased variant recovery with increased divergence. Variants were generally called with high accuracy, however identification of SNPs (single-nucleotide polymorphisms) was less accurate for high damage/low divergence samples. Modest increases in sequencing depth resulted in rapid gains in total variant recovery, and limited improvements to recovery of heterozygous variants.
conclusionsThis in silico study suggests aDNA-associated damage patterns minimally impact variant call accuracy and recovery from short-read alignment, while modest increases in sequencing depth can greatly improve variant recovery.
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