ArticlePloS one2017
Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data.
Article in PloS one, 2017. 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.
- Genomic analyses implicate noncoding de novo variants in congenital heart disease.Nature genetics · 2020Trial
- Development and Validation of a Scale for Measuring Leadership and Managerial Competencies of Middle Managers in Health Care and Medical Education in the Gulf Region: Cross-Sectional Study.JMIR medical education · 2026Article
- Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA.Scientific reports · 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
- Identification of grapevine clones via high-throughput amplicon sequencing: a proof-of-concept study.G3 (Bethesda, Md.) · 2023Article
- The Novel Structural Variation in the GHR Gene Is Associated with Growth Traits in Yaks (Animals : an open access journal from MDPI · 2023Article
- Multi-gene panel testing increases germline predisposing mutations' detection in a cohort of breast/ovarian cancer patients from Southern Italy.Frontiers in medicine · 2022Article
- Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels.Turkish journal of biology = Turk biyoloji dergisi · 2021Article
- INDEL detection, the 'Achilles heel' of precise genome editing: a survey of methods for accurate profiling of gene editing induced indels.Nucleic acids research · 2020Review
- Mutant Calreticulin in the Myeloproliferative Neoplasms.HemaSphere · 2020Review
- NGSEP3: accurate variant calling across species and sequencing protocols.Bioinformatics (Oxford, England) · 2019Article
- Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data.BMC bioinformatics · 2019Article
- Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics.Frontiers in genetics · 2019Review
- Genome-wide discovery of DNA polymorphisms among chickpea cultivars with contrasting seed size/weight and their functional relevance.Scientific reports · 2018Article
- Somatic mutagenesis in satellite cells associates with human skeletal muscle aging.Nature communications · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improvements demonstrated by the various sequencing platforms and analytical tools. However, there are still many errors associated with INDEL variant calling, and distinguishing INDELs from errors in NGS remains challenging. To evaluate INDEL calling from whole-exome sequencing (WES) data, we performed Sanger sequencing for all INDELs called from the several calling algorithm. We compared the performance of the four algorithms (i.e. GATK, SAMtools, Dindel, and Freebayes) for INDEL detection from the same sample. We examined the sensitivity and PPV of GATK (90.2 and 89.5%, respectively), SAMtools (75.3 and 94.4%, respectively), Dindel (90.1 and 88.6%, respectively), and Freebayes (80.1 and 94.4%, respectively). GATK had the highest sensitivity. Furthermore, we identified INDELs with high PPV (4 algorithms intersection: 98.7%, 3 algorithms intersection: 97.6%, and GATK and SAMtools intersection INDELs: 97.6%). We presented two key sources of difficulties in accurate INDEL detection: 1) the presence of repeat, and 2) heterozygous INDELs. Herein we could suggest the accessible algorithms that selectively reduce error rates and thereby facilitate INDEL detection. Our study may also serve as a basis for understanding the accuracy and completeness of INDEL detection.
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