ArticleHuman mutation2016
From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing.
Article in Human mutation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Systematic reanalysis of next-generation sequencing data in 101 neuromuscular disorder families enhances diagnostic yield, reveals intronic variants, and identifies a novel disease gene.Journal of neurology · 2026Article
- Genome Sequencing of Undiagnosed European Patients Suspected of Hereditary Cancer: Diagnostic Yield and Identification of Candidate Causative Variants.JCO precision oncology · 2026Article
- Genetically defined systemic autoinflammatory diseases in pediatric patients with Behçet's disease.Frontiers in immunology · 2026Article
- Review
- Phenotype-driven genomics enhance diagnosis in children with unresolved neuromuscular diseases.European journal of human genetics : EJHG · 2025Article
- Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses.Nature medicine · 2025Article
- Variants in mitochondrial disease genes are common causes of inherited peripheral neuropathies.Journal of neurology · 2024Article
- Identification and characterization of a new pathologic mutation in a large Leber hereditary optic neuropathy pedigree.Orphanet journal of rare diseases · 2024Article
- Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes.Nature communications · 2024Article
- Phenotypic similarity-based approach for variant prioritization for unsolved rare disease: a preliminary methodological report.European journal of human genetics : EJHG · 2024Article
- An interconnected data infrastructure to support large-scale rare disease research.GigaScience · 2024Article
- Functional Evidence ofInternational journal of molecular sciences · 2023Article
- Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases.Cell genomics · 2023Article
- Diagnostic Odyssey in an Adult Patient with Ophthalmologic Abnormalities and Hearing Loss: Contribution of RNA-Seq to the Diagnosis of a PEX1 Deficiency.International journal of molecular sciences · 2022Article
- The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species.Scientific reports · 2022Article
- The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases.Human mutation · 2022Article
- The importance of automation in genetic diagnosis: Lessons from analyzing an inherited retinal degeneration cohort with the Mendelian Analysis Toolkit (MATK).Genetics in medicine : official journal of the American College of Medical Genetics · 2022Article
- Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.European journal of human genetics : EJHG · 2021Article
- Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases.European journal of human genetics : EJHG · 2021Article
- Exome reanalysis and proteomic profiling identified TRIP4 as a novel cause of cerebellar hypoplasia and spinal muscular atrophy (PCH1).European journal of human genetics : EJHG · 2021Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next-generation sequencing as standard practice in research and diagnostics. However, computing cost-performance ratio is not advancing at an equivalent rate. Therefore, it is essential to evaluate the robustness of the variant detection process taking into account the computing resources required. We have benchmarked six combinations of state-of-the-art read aligners (BWA-MEM and GEM3) and variant callers (FreeBayes, GATK HaplotypeCaller, SAMtools) on whole genome and whole exome sequencing data from the NA12878 human sample. Results have been compared between them and against the NIST Genome in a Bottle (GIAB) variants reference dataset. We report differences in speed of up to 20 times in some steps of the process and have observed that SNV, and to a lesser extent InDel, detection is highly consistent in 70% of the genome. SNV, and especially InDel, detection is less reliable in 20% of the genome, and almost unfeasible in the remaining 10%. These findings will aid in choosing the appropriate tools bearing in mind objectives, workload, and computing infrastructure available.
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Registered trials
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.