ArticlePloS one2023
Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools.
Article in PloS one, 2023. 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.
- Whole exome sequencing identifies somatically mutated genes in bladder cancer: A pilot study from Bangladesh.Biochemistry and biophysics reports · 2026Article
- Genome-Wide Identification of Candidate Genes Associated with Antler Weight in Tahe Red Deer.Animals : an open access journal from MDPI · 2026Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- Osteogenesis Imperfecta with a gross deletion including theBone reports · 2026Article
- Accurate detections of the heterozygous SNPs with rice genomic data and prediction of de novo spontaneous mutation rate.Plant methods · 2025Article
- Whole Genome Resequencing Reveals the Genetic Basis of Desert Arid Climate Adaptation in Lop Sheep.Animals : an open access journal from MDPI · 2025Article
- Genomic landscape of hormone therapy-resistant HR-positive, HER2-negative breast cancer.Breast cancer research and treatment · 2025Article
- Article
- Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets.Scientific reports · 2025Article
- Article
- Identification of Ovarian High-Grade Serous Carcinoma with Mitochondrial Gene Variation.International journal of molecular sciences · 2025Article
- Benchmarking accelerated next-generation sequencing analysis pipelines.Bioinformatics advances · 2025Article
- Article
- Article
- Temporal sex specific brain gene expression pattern during early rat embryonic development.Frontiers in cell and developmental biology · 2024Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The next-generation sequencing (NGS) technology represents a significant advance in genomics and medical diagnosis. Nevertheless, the time it takes to perform sequencing, data analysis, and variant interpretation is a bottleneck in using next-generation sequencing in precision medicine. For accurate and efficient performance in clinical diagnostic lab practice, a consistent data analysis pipeline is necessary to avoid false variant calls and achieve optimum accuracy. This study aims to compare the performance of two NGS data analysis pipeline compartments, including short-read mapping (BWA-MEM and BWA-MEM2) and variant calling (GATK-HaplotypeCaller and DRAGEN-GATK). On Whole Exome Sequencing (WES) data, computational performance was assessed using several criteria, including mapping efficiency, variant calling performance, false positive calls rate, and time. We examined four gold-standard WES data sets: Ashkenazim father (NA24149), Ashkenazim mother (NA24143), Ashkenazim son (NA24385), and Asian son (NA25631). In addition, eighteen exome samples were analyzed based on different read counts, and coverage was used precisely in the run-time assessment. By using BWA-MEM 2 and Dragen-GATK, this study achieved faster and more accurate detection for SNVs and indels than the standard GATK Best Practices workflow. This systematic comparison will enable the bioinformatics community to develop a more efficient and faster solution for analyzing NGS data.
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