ArticleMicrobial genomics2021
Generalizable characteristics of false-positive bacterial variant calls.
Article in Microbial genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Resistance to disinfection emerges inCurrent research in microbial sciences · 2026Article
- High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV.Genome research · 2026Article
- A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producingMicrobial genomics · 2026Article
- Accurate detections of the heterozygous SNPs with rice genomic data and prediction of de novo spontaneous mutation rate.Plant methods · 2025Article
- High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV.bioRxiv : the preprint server for biology · 2025Article
- Investigation and pathogenetic testing of Shewanella spp. positive diarrhea cases in Beijing, China.Scientific reports · 2025Article
- Adaptive laboratory-evolved MRSA with PPEF manifests cross-susceptibility to oxacillin and hypersensitivity to ciprofloxacin.Microbiology spectrum · 2025Article
- Constraints in temperature adaptation reinforce differences in thermal niche between mesophilic and psychrotolerantProceedings. Biological sciences · 2025Article
- Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA).Molecular biology and evolution · 2025Article
- A genomic and phenotypic investigation of pigeon-adaptive Salmonella.PLoS pathogens · 2025Article
- Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data.eLife · 2024Article
- SynonymousNAR genomics and bioinformatics · 2024Article
- A new concept of biocatalytic synthesis of acrylic monomers for obtaining water-soluble acrylic heteropolymers.Metabolic engineering communications · 2024Article
- Whole genome sequencing distinguishes skin colonizing from infection-associatedFrontiers in cellular and infection microbiology · 2024Article
- The complex genomic diversity ofEcology and evolution · 2023Article
- Emergence and Evolution of OXA-23-Producing ST46Antibiotics (Basel, Switzerland) · 2023Article
- Evolutionary and genomic insights into the long-term colonization ofEmerging microbes & infections · 2022Article
- Description of a Rare Pyomelanin-Producing Carbapenem-Resistant Acinetobacter baumannii Strain Coharboring Chromosomal OXA-23 and NDM-1.Microbiology spectrum · 2022Article
- Identification of novel, crypticMicrobial genomics · 2022Article
- Antibiotic resistance and genomic features ofPeerJ · 2022Article
Corrections and comments
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Authors and funding
1 author.
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Abstract
Minimizing false positives is a critical issue when variant calling as no method is without error. It is common practice to post-process a variant-call file (VCF) using hard filter criteria intended to discriminate true-positive (TP) from false-positive (FP) calls. These are applied on the simple principle that certain characteristics are disproportionately represented among the set of FP calls and that a user-chosen threshold can maximize the number detected. To provide guidance on this issue, this study empirically characterized all false SNP and indel calls made using real Illumina sequencing data from six disparate species and 166 variant-calling pipelines (the combination of 14 read aligners with up to 13 different variant callers, plus four 'all-in-one' pipelines). We did not seek to optimize filter thresholds but instead to draw attention to those filters of greatest efficacy and the pipelines to which they may most usefully be applied. In this respect, this study acts as a coda to our previous benchmarking evaluation of bacterial variant callers, and provides general recommendations for effective practice. The results suggest that, of the pipelines analysed in this study, the most straightforward way of minimizing false positives would simply be to use Snippy. We also find that a disproportionate number of false calls, irrespective of the variant-calling pipeline, are located in the vicinity of indels, and highlight this as an issue for future development.
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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.