ArticleBioinformatics (Oxford, England)2018
SV2: accurate structural variation genotyping and de novo mutation detection from whole genomes.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data.Genome biology · 2026Article
- Long-read genome sequencing improves detection and functional interpretation of structural and repeat variants in autism.Cell genomics · 2026Article
- The promise and challenges of characterizing genome-wide structural variants: A case study in a critically endangered parrot.Molecular ecology resources · 2025Article
- Investigating copy number variants in schizophrenia pedigrees using a new consensus pipeline called PECAN.Scientific reports · 2024Article
- NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data.Bioinformatics (Oxford, England) · 2024Article
- Detection of trait-associated structural variations using short-read sequencing.Cell genomics · 2023Article
- Regulatory de novo mutations underlying intellectual disability.Life science alliance · 2023Article
- A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex.Nature genetics · 2022Article
- Combining callers improves the detection of copy number variants from whole-genome sequencing.European journal of human genetics : EJHG · 2022Article
- De novo mutations identified by whole-genome sequencing implicate chromatin modifications in obsessive-compulsive disorder.Science advances · 2022Article
- Population-scale genotyping of structural variation in the era of long-read sequencing.Computational and structural biotechnology journal · 2022Review
- NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data.GigaScience · 2021Article
- Samplot: a platform for structural variant visual validation and automated filtering.Genome biology · 2021Article
- Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques.Molecular biology and evolution · 2021Article
- The Emerging Genetic Landscape of Hirschsprung Disease and Its Potential Clinical Applications.Frontiers in pediatrics · 2021Review
- A random forest-based framework for genotyping and accuracy assessment of copy number variations.NAR genomics and bioinformatics · 2020Article
- Paragraph: a graph-based structural variant genotyper for short-read sequence data.Genome biology · 2019Article
- Evaluation of computational genotyping of structural variation for clinical diagnoses.GigaScience · 2019Article
- Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome.PLoS computational biology · 2019Article
- Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Motivation: Structural variation (SV) detection from short-read whole genome sequencing is error prone, presenting significant challenges for population or family-based studies of disease. Results: Here, we describe SV2, a machine-learning algorithm for genotyping deletions and duplications from paired-end sequencing data. SV2 can rapidly integrate variant calls from multiple structural variant discovery algorithms into a unified call set with high genotyping accuracy and capability to detect de novo mutations. Availability and implementation: SV2 is freely available on GitHub (https://github.com/dantaki/SV2). Contact: jsebat@ucsd.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
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