ArticlePLoS computational biology2022
Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 26 citations in OpenAlex.
- Pangenomes aid accurate detection of large insertions and deletions from targeted sequencing: the case of cardiomyopathies.Genome medicine · 2026Article
- A portable recalibration workflow for reference-based variant calling in non-human genomes.PLoS computational biology · 2026Article
- Emerging role of DNA polymerase epsilon non-exonuclease domain mutations in colorectal cancer: From sequence variants to clinical implications.World journal of gastroenterology · 2026Article
- MOV&RSim: computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation.BMC bioinformatics · 2025Article
- A comparative review of short genetic variant databases across humans and animal species.Briefings in bioinformatics · 2025Review
- Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies.Human vaccines & immunotherapeutics · 2024Review
- Utilizing insights of DNA repair machinery to discover MMEJ deletions and novel mechanisms.Nucleic acids research · 2024Article
- Unravelling mutational signatures with plasma circulating tumour DNA.Nature communications · 2024Article
- Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking.BMC bioinformatics · 2024Article
- Comparative evaluation of SNVs, indels, and structural variations detected with short- and long-read sequencing data.Human genome variation · 2024Article
- Histologic and Genomic Analysis of Conjunctival SCC in African and American Cohorts Reveal UV Light and HPV Signatures and High Tumor Mutation Burden.Investigative ophthalmology & visual science · 2024Article
- Hereditary Renal Cancer Syndromes.Medical sciences (Basel, Switzerland) · 2024Review
- VarSCAT: A computational tool for sequence context annotations of genomic variants.PLoS computational biology · 2023Article
- Tumour purity as an underlying key factor in tumour mutation detection in colorectal cancer.Clinical and translational medicine · 2023Article
- Optimized high-throughput screening of non-coding variants identified from genome-wide association studies.Nucleic acids research · 2023Article
- Persistence of a Frameshifting Deletion in SARS-CoV-2 ORF7a for the Duration of a Major Outbreak.Viruses · 2023Article
- Optimizing Insertion and Deletion Detection Using Next-Generation Sequencing in the Clinical Laboratory.The Journal of molecular diagnostics : JMD · 2022Article
- Fungal Strains with Identical Genomes Were Found at a Distance of 2000 Kilometers after 40 Years.Journal of fungi (Basel, Switzerland) · 2022Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Insertions and deletions (indels) in human genomes are associated with a wide range of phenotypes, including various clinical disorders. High-throughput, next generation sequencing (NGS) technologies enable the detection of short genetic variants, such as single nucleotide variants (SNVs) and indels. However, the variant calling accuracy for indels remains considerably lower than for SNVs. Here we present a comparative study of the performance of variant calling tools for indel calling, evaluated with a wide repertoire of NGS datasets. While there is no single optimal tool to suit all circumstances, our results demonstrate that the choice of variant calling tool greatly impacts the precision and recall of indel calling. Furthermore, to reliably detect indels, it is essential to choose NGS technologies that offer a long read length and high coverage coupled with specific variant calling tools.
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