ArticleScientific reports2022
The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp.International journal of molecular sciences · 2026Article
- A single-cell transcriptome atlas reveals paradoxical monoallelic expression of RNA editing and heterozygous SNPs.Nucleic acids research · 2026Article
- Integrating Mutation-Derived and Expression Features from Single-Cell RNA Sequencing: Pitfalls of Standard Cross-Validation in Small-Cohort Settings.International journal of molecular sciences · 2026Article
- Benchmarking genomic variant calling tools in inbred mouse strains: recommendations and considerations.Genetics · 2026Article
- Retrotransposed gene copies persist under relaxed selection in wild Spodoptera frugiperda.Molecular biology and evolution · 2026Article
- Silent Erosion: Impact of Forest Logging on Genetic Diversity in Tropical Understorey Birds.Genome biology and evolution · 2026Article
- Using pangenome variation graphs to improve mutation detection in a large DNA virus.Microbial genomics · 2026Article
- Exploring Genomic Variability in the Mediterranean Buffalo Breed: A Step Towards Custom SNP Array.Animals : an open access journal from MDPI · 2026Article
- Genome-wide association study bridging genomics-phenomics gap in natural plant populations.Journal of applied genetics · 2026Review
- Polymorphisms and Expression Characteristics of theAnimals : an open access journal from MDPI · 2026Article
- Alternative splicing contributes to plasticity and regulatory divergence in locally adapted house mice from the Americas.Molecular biology and evolution · 2026Article
- Review
- Convergent evolution of sex chromosomes in two palm species, Phoenix dactylifera and Kerriodoxa elegans.Annals of botany · 2025Article
- Relaxation of selective constraint on the sweet-taste receptor gene TAS1R2 in lorisiform primates.Scientific reports · 2025Article
- Assessing Genotype Imputation Methods for Low-Coverage Sequencing Data in Populations With Differing Relatedness and Inbreeding Levels.Molecular ecology resources · 2025Article
- Accurate detections of the heterozygous SNPs with rice genomic data and prediction of de novo spontaneous mutation rate.Plant methods · 2025Article
- Order from entropy: big data from FAIR data cohorts in the digital age of plant breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Learning-based parallel acceleration for HaplotypeCaller.BMC bioinformatics · 2025Article
- A 17.1 kb duplication downstream GATA6 is strongly associated with egg weight in chicken.BMC genomics · 2025Article
- Article
Corrections and comments
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identification of genetic variations is a central part of population and quantitative genomics studies based on high-throughput sequencing data. Even though popular variant callers such as Bcftools mpileup and GATK HaplotypeCaller were developed nearly 10 years ago, their performance is still largely unknown for non-human species. Here, we showed by benchmark analyses with a simulated insect population that Bcftools mpileup performs better than GATK HaplotypeCaller in terms of recovery rate and accuracy regardless of mapping software. The vast majority of false positives were observed from repeats, especially for GATK HaplotypeCaller. Variant scores calculated by GATK did not clearly distinguish true positives from false positives in the vast majority of cases, implying that hard-filtering with GATK could be challenging. These results suggest that Bcftools mpileup may be the first choice for non-human studies and that variants within repeats might have to be excluded for downstream analyses.
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