ArticleHuman genomics2015
Performance evaluation of indel calling tools using real short-read data.
Article in Human genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 110 citations in OpenAlex.
- A universal indel filtering workflow for both long-read and short-read NGS data.BMC research notes · 2026Article
- Synth4bench: generating synthetic data for benchmarking tumor-only somatic variant calling algorithms.Frontiers in bioinformatics · 2026Article
- Indel calling from ONT sequencing data of family trios via sparse attention and 3D convolution.Briefings in bioinformatics · 2025Article
- CaMutQC: An R package for integrative quality control and filtration of cancer somatic mutations.Computational and structural biotechnology journal · 2025Article
- Evolutionary Dynamics of Accelerated Antiviral Resistance Development in Hypermutator Herpesvirus.Molecular biology and evolution · 2024Article
- Comparative evaluation of SNVs, indels, and structural variations detected with short- and long-read sequencing data.Human genome variation · 2024Article
- Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project.Scientific reports · 2024Article
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- XCVATR: detection and characterization of variant impact on the Embeddings of single -cell and bulk RNA-sequencing samples.BMC genomics · 2022Article
- Optimizing Insertion and Deletion Detection Using Next-Generation Sequencing in the Clinical Laboratory.The Journal of molecular diagnostics : JMD · 2022Article
- Genomic Approaches to Uncovering the Coevolutionary History of Parasitic Lice.Life (Basel, Switzerland) · 2022Review
- A comprehensive benchmarking of WGS-based deletion structural variant callers.Briefings in bioinformatics · 2022Article
- Small Insertions and Deletions Drive Genomic Plasticity during Adaptive Evolution of Yersinia pestis.Microbiology spectrum · 2022Review
- Genomic and transcriptomic-based analysis of agronomic traits in sugar beet (Frontiers in plant science · 2022Article
- Structural and functional analysis of somatic coding and UTR indels in breast and lung cancer genomes.Scientific reports · 2021Article
- Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs.BMC genomics · 2021Article
- Reversible gene silencing through frameshift indels and frameshift scars provide adaptive plasticity for Mycobacterium tuberculosis.Nature communications · 2021Article
- Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes.Genetics, selection, evolution : GSE · 2021Article
- Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels.BMC bioinformatics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundInsertion and deletion (indel), a common form of genetic variation, has been shown to cause or contribute to human genetic diseases and cancer. With the advance of next-generation sequencing technology, many indel calling tools have been developed; however, evaluation and comparison of these tools using large-scale real data are still scant. Here we evaluated seven popular and publicly available indel calling tools, GATK Unified Genotyper, VarScan, Pindel, SAMtools, Dindel, GTAK HaplotypeCaller, and Platypus, using 78 human genome low-coverage data from the 1000 Genomes project.
resultsComparing indels called by these tools with a known set of indels, we found that Platypus outperforms other tools. In addition, a high percentage of known indels still remain undetected and the number of common indels called by all seven tools is very low.
conclusionAll these findings indicate the necessity of improving the existing tools or developing new algorithms to achieve reliable and consistent indel calling results.
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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.