ArticleScientific reports2020
Accuracy and efficiency of germline variant calling pipelines for human genome data.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 121 citations in OpenAlex.
- High-Penetrance Rare Variants Underlying Familial Lung Cancer Risk: Insights From Genetic Epidemiology of Lung Cancer Consortium.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2026Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- Familial Oculoauriculovertebral Spectrum: A Genomic Investigation of Autosomal Dominant Inheritance.The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association · 2026Article
- Exploring Genomic Variability in the Mediterranean Buffalo Breed: A Step Towards Custom SNP Array.Animals : an open access journal from MDPI · 2026Article
- Disorders of sex development associated with MPI and RSPH1 variants expand the phenotypic spectrum of CDG and PCD in Morocco.Molecular biology reports · 2026Article
- CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts.Bioinformatics advances · 2026Article
- Residual allelic activity likely underlies the low rates of disease expression for predicted loss-of-function variants in population-scale biobanks.American journal of human genetics · 2025Article
- MOV&RSim: computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation.BMC bioinformatics · 2025Article
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- Comprehensive assessment of whole-genome sequencing-based variant calling pipelines in monozygotic twins.Briefings in bioinformatics · 2025Article
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- Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain.Genome research · 2025Article
- A population-based analysis of the molecular landscape of glioma in adolescents and young adults reveals insights into gliomagenesis.Nature cancer · 2025Article
- UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP.Genomics, proteomics & bioinformatics · 2025Article
- Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors.Nature medicine · 2025Article
- Neoadjuvant triplet immune checkpoint blockade in newly diagnosed glioblastoma.Nature medicine · 2025Article
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- Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets.Scientific reports · 2025Article
- Whole exome sequencing reveals ABCD1 variant as a potential contributor to male infertility.Molecular biology reports · 2025Article
- Benchmarking accelerated next-generation sequencing analysis pipelines.Bioinformatics advances · 2025Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advances in next-generation sequencing technology have enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into how genetic polymorphisms affect disease phenotypes. The development of different bioinformatics pipelines has continuously improved the variant analysis of WGS data. However, there is a necessity for a systematic performance comparison of these pipelines to provide guidance on the application of WGS-based scientific and clinical genomics. In this study, we evaluated the performance of three variant calling pipelines (GATK, DRAGEN and DeepVariant) using the Genome in a Bottle Consortium, "synthetic-diploid" and simulated WGS datasets. DRAGEN and DeepVariant show better accuracy in SNP and indel calling, with no significant differences in their F1-score. DRAGEN platform offers accuracy, flexibility and a highly-efficient execution speed, and therefore superior performance in the analysis of WGS data on a large scale. The combination of DRAGEN and DeepVariant also suggests a good balance of accuracy and efficiency as an alternative solution for germline variant detection in further applications. Our results facilitate the standardization of benchmarking analysis of bioinformatics pipelines for reliable variant detection, which is critical in genetics-based medical research and clinical applications.
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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.