ReviewHuman mutation2022
Variant calling: Considerations, practices, and developments.
Review in Human mutation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- ClinicalFrontiers in microbiology · 2025Pooled it
- Long-read based detection of large copy number variants with potential functional significance using the ContextSV structural variant caller.NAR genomics and bioinformatics · 2026Article
- Pansoma, a machine learning tool for identifying somatic variants using pangenome graphs.bioRxiv : the preprint server for biology · 2026Article
- Tutorial for variant interrogation in tumor samples.PLoS computational biology · 2026Article
- CHIP ahoy: charting a decade of discovery in clonal hematopoiesis.Haematologica · 2026Review
- Exploring the genetic landscape of COVID-19 susceptibility and severity among patients in Türkiye.BMC medical genomics · 2025Article
- A library of avian proteins improves palaeoproteomic taxonomic identification and reveals widespread intraspecies variability.Nature communications · 2025Article
- Next-Generation Sequencing: A Review of Its Transformative Impact on Cancer Diagnosis, Treatment, and Resistance Management.Diagnostics (Basel, Switzerland) · 2025Review
- Precise detection of differential RNA editing sites across varied biological conditions using the CADRES pipeline.Scientific reports · 2025Article
- Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars.BMC genomics · 2025Article
- Cancer genomics and bioinformatics in Latin American countries: applications, challenges, and perspectives.Frontiers in oncology · 2025Review
- Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data.Human genomics · 2024Review
- Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics.Scientific reports · 2024Article
- Improving somatic exome sequencing performance by biological replicates.BMC bioinformatics · 2024Article
- Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.Viruses · 2024Article
- Current and future trends in whole genome sequencing in cancer.Cancer biology & medicine · 2024Review
- Can long-read sequencing tackle the barriers, which the next-generation could not? A review.Pathology oncology research : POR · 2024Review
- Differential tumor immune microenvironment coupled with tumor progression or tumor eradication in HPV-antigen expressing squamous cell carcinoma (SCC) models.Frontiers in immunology · 2024Article
- Concerning the eXclusion in human genomics: the choice of sex chromosome representation in the human genome drastically affects the number of identified variants.G3 (Bethesda, Md.) · 2023Article
- Concerning the eXclusion in human genomics: The choice of sex chromosome representation in the human genome drastically affects number of identified variants.bioRxiv : the preprint server for biology · 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
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The success of many clinical, association, or population genetics studies critically relies on properly performed variant calling step. The variety of modern genomics protocols, techniques, and platforms makes our choices of methods and algorithms difficult and there is no "one size fits all" solution for study design and data analysis. In this review, we discuss considerations that need to be taken into account while designing the study and preparing for the experiments. We outline the variety of variant types that can be detected using sequencing approaches and highlight some specific requirements and basic principles of their detection. Finally, we cover interesting developments that enable variant calling for a broad range of applications in the genomics field. We conclude by discussing technological and algorithmic advances that have the potential to change the ways of calling DNA variants in the nearest future.
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.