ArticleNucleic acids research2016
A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- A comparative study of structural variant calling in WGS from Alzheimer's disease families.Life science alliance · 2024Article
- Joint inference of clonal structure using single-cell genome and transcriptome sequencing data.NAR genomics and bioinformatics · 2024Article
- High-resolution mapping reveals the mechanism and contribution of genome insertions and deletions to RNA virus evolution.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes.Nucleic acids research · 2019Article
- SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.GigaScience · 2018Article
- Identification of large rearrangements in cancer genomes with barcode linked reads.Nucleic acids research · 2018Article
- Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping.Frontiers in plant science · 2018Article
- Discovery and genotyping of novel sequence insertions in many sequenced individuals.Bioinformatics (Oxford, England) · 2017Article
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Authors and funding
8 authors.
Funding
Abstract
We present SWAN, a statistical framework for robust detection of genomic structural variants in next-generation sequencing data and an analysis of mid-range size insertion and deletions (<10 Kb) for whole genome analysis and DNA mixtures. To identify these mid-range size events, SWAN collectively uses information from read-pair, read-depth and one end mapped reads through statistical likelihoods based on Poisson field models. SWAN also uses soft-clip/split read remapping to supplement the likelihood analysis and determine variant boundaries. The accuracy of SWAN is demonstrated by in silico spike-ins and by identification of known variants in the NA12878 genome. We used SWAN to identify a series of novel set of mid-range insertion/deletion detection that were confirmed by targeted deep re-sequencing. An R package implementation of SWAN is open source and freely available.
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Registered trials
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