ArticleScientific reports2022
Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- Convergence of machine learning and genomics for precision oncology.Nature reviews. Cancer · 2026Review
- Multi-ancestry exome-wide study identifies variants associated with Alzheimer's disease protection.Journal of Alzheimer's disease : JAD · 2026Article
- GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis.Briefings in bioinformatics · 2026Article
- Genetics to Improve Outcomes in Schizophrenia (GENios): A within-case molecular genetic study protocol.PloS one · 2026Article
- Familial Hypercholesterolemia: Prevalence and Discrepancy between Genotype and Phenotype. Findings of the Population-based Hamburg City Health Study.Deutsches Arzteblatt international · 2025Observational
- Performance comparison of germline variant calling tools in sporadic disease cohorts.Molecular genetics and genomics : MGG · 2025Article
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- Experience in developing the human genome standard E701.NAR genomics and bioinformatics · 2025Article
- A benchmark study of compression software for human short-read sequence data.Scientific reports · 2025Article
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- Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets.Scientific reports · 2025Article
- Merging High-Throughput, Amplicon-Based Second and Third Generation Sequencing Data: An Integrative and Modular Data Analysis Framework for Haplotype Prediction and Output Evaluation.International journal of molecular sciences · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Benchmarking accelerated next-generation sequencing analysis pipelines.Bioinformatics advances · 2025Article
- Cancer genomics and bioinformatics in Latin American countries: applications, challenges, and perspectives.Frontiers in oncology · 2025Review
- Rare disease genomics and precision medicine.Genomics & informatics · 2024Review
- Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid advances in high-throughput DNA sequencing technologies have enabled the conduct of whole genome sequencing (WGS) studies, and several bioinformatics pipelines have become available. The aim of this study was the comparison of 6 WGS data pre-processing pipelines, involving two mapping and alignment approaches (GATK utilizing BWA-MEM2 2.2.1, and DRAGEN 3.8.4) and three variant calling pipelines (GATK 4.2.4.1, DRAGEN 3.8.4 and DeepVariant 1.1.0). We sequenced one genome in a bottle (GIAB) sample 70 times in different runs, and one GIAB trio in triplicate. The truth set of the GIABs was used for comparison, and performance was assessed by computation time, F
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