ArticleScientific reports2017
Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers, 1 of them a synthesis that pooled it.
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Who cites it
113 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Deep learning approaches for resolving genomic discrepancies in cancer: a systematic review and clinical perspective.Briefings in bioinformatics · 2025Pooled it
- Clonal Hematopoiesis and Cardiovascular Disease and Bleeding Risk and the Effectiveness of Aspirin.JAMA cardiology · 2025Trial
- Not Missing the Notch: Detection Challenges of Juxtamembrane NOTCH1 Variant Detection in T-Cell Acute Lymphoblastic Leukemia.Journal of clinical laboratory analysis · 2026Article
- Genome-wide association study bridging genomics-phenomics gap in natural plant populations.Journal of applied genetics · 2026Review
- Synth4bench: generating synthetic data for benchmarking tumor-only somatic variant calling algorithms.Frontiers in bioinformatics · 2026Article
- Comprehensive assessment of whole-genome sequencing-based variant calling pipelines in monozygotic twins.Briefings in bioinformatics · 2025Article
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- Recurrent spontaneous miscarriages from sperm after ABVD chemotherapy in a patient with Hodgkin's lymphoma: sperm DNA and methylation profiling.Asian journal of andrology · 2025Article
- The Role of Somatic Mutation in Hereditary Hemorrhagic Telangiectasia Pathogenesis.Journal of clinical medicine · 2025Review
- Transposon DNA sequences facilitate the tissue-specific gene transfer of circulating tumor DNA between human cells.Nucleic acids research · 2024Article
- Differential requirement for RecFOR pathway components in Thermus thermophilus.Environmental microbiology reports · 2024Article
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- ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation.Bioinformatics (Oxford, England) · 2024Article
- Performance analysis of conventional and AI-based variant callers using short and long reads.BMC bioinformatics · 2023Article
- Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater.International journal of molecular sciences · 2023Article
- Evaluating the performance of low-frequency variant calling tools for the detection of variants from short-read deep sequencing data.Scientific reports · 2023Article
- Non-random mating within an Island rookery of Hawaiian hawksbill turtles: demographic discontinuity at a small coastline scale.Royal Society open science · 2023Article
- Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data.Genome biology · 2023Article
- satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect.Genome biology · 2023Article
53 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Valid variant calling results are crucial for the use of next-generation sequencing in clinical routine. However, there are numerous variant calling tools that usually differ in algorithms, filtering strategies, recommendations and thus, also in the output. We evaluated eight open-source tools regarding their ability to call single nucleotide variants and short indels with allelic frequencies as low as 1% in non-matched next-generation sequencing data: GATK HaplotypeCaller, Platypus, VarScan, LoFreq, FreeBayes, SNVer, SAMtools and VarDict. We analysed two real datasets from patients with myelodysplastic syndrome, covering 54 Illumina HiSeq samples and 111 Illumina NextSeq samples. Mutations were validated by re-sequencing on the same platform, on a different platform and expert based review. In addition we considered two simulated datasets with varying coverage and error profiles, covering 50 samples each. In all cases an identical target region consisting of 19 genes (42,322 bp) was analysed. Altogether, no tool succeeded in calling all mutations. High sensitivity was always accompanied by low precision. Influence of varying coverages- and background noise on variant calling was generally low. Taking everything into account, VarDict performed best. However, our results indicate that there is a need to improve reproducibility of the results in the context of multithreading.
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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.