ArticleScientific reports2019
Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
50 citing papers in PubMed.
- Artificial Intelligence and Genomic Data Analysis: New Frontiers in Precision Medicine.International journal of molecular sciences · 2026Review
- Improved genotype inference reveals cis- and trans-driven variation in the loss-of-heterozygosity rates in yeast.Genetics · 2026Article
- The Mutation Patterns of MET Gene in Lung Cancer and Brain Tumors: Clinical and Therapeutic Implications.Cancer medicine · 2026Article
- Genome resequencing and custom genotyping elucidates the origin and dissemination history of an emblematic grapevine cultivar, 'Tempranillo Tinto'.Horticulture research · 2025Article
- Comprehensive assessment of whole-genome sequencing-based variant calling pipelines in monozygotic twins.Briefings in bioinformatics · 2025Article
- Accurate detections of the heterozygous SNPs with rice genomic data and prediction of de novo spontaneous mutation rate.Plant methods · 2025Article
- Enhancing public health surveillance: a comparative study of platform-specific and hybrid assembly approaches in SARS-CoV-2 genome sequencing.Microbial genomics · 2025Article
- Integrated analysis of oral rinse-derived and plasma circulating tumour DNA for mutation profiling and outcome prediction with oral squamous cell carcinoma.NPJ precision oncology · 2025Article
- Rapid Whole-Genome Sequencing in Critically Ill Infants and Children with Suspected, Undiagnosed Genetic Diseases: Evolution to a First-Tier Clinical Laboratory Test in the Era of Precision Medicine.Children (Basel, Switzerland) · 2025Review
- cascAGS: Comparative Analysis of SNP Calling Methods for Human Genome Data in the Absence of Gold Standard.Interdisciplinary sciences, computational life sciences · 2025Article
- Article
- Distribution of EGFR fusions in 35,023 Chinese patients with solid tumors-the frequency, fusion partners and clinical outcome.World journal of surgical oncology · 2024Article
- Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling.BMC bioinformatics · 2024Article
- Molecular and immunological characteristics of postoperative relapse in lymph node-positive esophageal squamous cell cancer.Cancer medicine · 2024Article
- A comparative investigation of single nucleotide variant calling for a personal non-Caucasian sequencing sample.Genes & genomics · 2023Article
- Molecular genomic landscape of pediatric solid tumors in Chinese patients: implications for clinical significance.Journal of cancer research and clinical oncology · 2023Article
- Short-read aligner performance in germline variant identification.Bioinformatics (Oxford, England) · 2023Review
- Age-dependent genomic characteristics and their impact on immunotherapy in lung adenocarcinoma.Journal of cancer research and clinical oncology · 2023Article
- Performance comparisons between clustering models for reconstructing NGS results from technical replicates.Frontiers in genetics · 2023Article
- Comprehensive genomic analysis of primary bone sarcomas reveals different genetic patterns compared with soft tissue sarcomas.Frontiers in oncology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Comprehensive and accurate detection of variants from whole-genome sequencing (WGS) is a strong prerequisite for translational genomic medicine; however, low concordance between analytic pipelines is an outstanding challenge. We processed a European and an African WGS samples with 70 analytic pipelines comprising the combination of 7 short-read aligners and 10 variant calling algorithms (VCAs), and observed remarkable differences in the number of variants called by different pipelines (max/min ratio: 1.3~3.4). The similarity between variant call sets was more closely determined by VCAs rather than by short-read aligners. Remarkably, reported minor allele frequency had a substantial effect on concordance between pipelines (concordance rate ratio: 0.11~0.92; Wald tests, P < 0.001), entailing more discordant results for rare and novel variants. We compared the performance of analytic pipelines and pipeline ensembles using gold-standard variant call sets and the catalog of variants from the 1000 Genomes Project. Notably, a single pipeline using BWA-MEM and GATK-HaplotypeCaller performed comparable to the pipeline ensembles for 'callable' regions (~97%) of the human reference genome. While a single pipeline is capable of analyzing common variants in most genomic regions, our findings demonstrated the limitations and challenges in analyzing rare or novel variants, especially for non-European genomes.
Indexed as
Identifiers
What OpenQuestion holds
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.