ArticleBMC genomics2022
Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 19 citations in OpenAlex.
- Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources.Genome research · 2026Article
- AutoMethyc: an automated methylation analysis for massively parallel sequencing data.Briefings in bioinformatics · 2025Article
- Sperm DNA methylation landscape and its links to male fertility in a non-model teleost using EM-seq.Heredity · 2025Article
- Integration of epigenomic and genomic data to predict residual feed intake and the feed conversion ratio in dairy sheep via machine learning algorithms.BMC genomics · 2025Article
- DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation.Genome medicine · 2025Article
- DNA Methylation Carries Signatures of Sublethal Effects Under Thermal Stress in Loggerhead Sea Turtles.Evolutionary applications · 2024Article
- Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies.Briefings in bioinformatics · 2024Article
- Methylation marks in blood DNA reveal breast cancer risk in patients fulfilling hereditary disease criteria.NPJ precision oncology · 2024Article
- Mixed Patterns of Intergenerational DNA Methylation Inheritance in Acropora.Molecular biology and evolution · 2024Article
- Comprehensive DNA Methylation Analysis Indicates That Pancreatic Intraepithelial Neoplasia Lesions Are Acinar-Derived and Epigenetically Primed for Carcinogenesis.Cancer research · 2023Article
- On the causes of gene-body methylation variation in Arabidopsis thaliana.PLoS genetics · 2023Article
- Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects.Molecular biology and evolution · 2023Article
- epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.Molecular ecology resources · 2022Article
- Performance of methods to detect genetic variants from bisulphite sequencing data in a non-model species.Molecular ecology resources · 2022Article
- EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.NAR genomics and bioinformatics · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 5 countries.
Funding
Abstract
backgroundCalling germline SNP variants from bisulfite-converted sequencing data poses a challenge for conventional software, which have no inherent capability to dissociate true polymorphisms from artificial mutations induced by the chemical treatment. Nevertheless, SNP data is desirable both for genotyping and to understand the DNA methylome in the context of the genetic background. The confounding effect of bisulfite conversion however can be conceptually resolved by observing differences in allele counts on a per-strand basis, whereby artificial mutations are reflected by non-complementary base pairs.
resultsHerein, we present a computational pre-processing approach for adapting sequence alignment data, thus indirectly enabling downstream analysis on a per-strand basis using conventional variant calling software such as GATK or Freebayes. In comparison to specialised tools, the method represents a marked improvement in precision-sensitivity based on high-quality, published benchmark datasets for both human and model plant variants.
conclusionThe presented "double-masking" procedure represents an open source, easy-to-use method to facilitate accurate variant calling using conventional software, thus negating any dependency on specialised tools and mitigating the need to generate additional, conventional sequencing libraries alongside bisulfite sequencing experiments. The method is available at https://github.com/bio15anu/revelio and an implementation with Freebayes is available at https://github.com/EpiDiverse/SNP.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.