LUMPY: a probabilistic framework for structural variant discovery
- PMID: 24970577
- PMCID: PMC4197822
- DOI: 10.1186/gb-2014-15-6-r84
LUMPY: a probabilistic framework for structural variant discovery
Abstract
Comprehensive discovery of structural variation (SV) from whole genome sequencing data requires multiple detection signals including read-pair, split-read, read-depth and prior knowledge. Owing to technical challenges, extant SV discovery algorithms either use one signal in isolation, or at best use two sequentially. We present LUMPY, a novel SV discovery framework that naturally integrates multiple SV signals jointly across multiple samples. We show that LUMPY yields improved sensitivity, especially when SV signal is reduced owing to either low coverage data or low intra-sample variant allele frequency. We also report a set of 4,564 validated breakpoints from the NA12878 human genome. https://github.com/arq5x/lumpy-sv.
Figures
Similar articles
-
SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability.Bioinformatics. 2016 Apr 1;32(7):984-92. doi: 10.1093/bioinformatics/btv751. Epub 2016 Jan 6. Bioinformatics. 2016. PMID: 26740523 Free PMC article.
-
Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms.Brief Bioinform. 2016 Jan;17(1):51-62. doi: 10.1093/bib/bbv028. Epub 2015 May 20. Brief Bioinform. 2016. PMID: 25998133
-
LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data.Nat Commun. 2019 Dec 6;10(1):5585. doi: 10.1038/s41467-019-13397-7. Nat Commun. 2019. PMID: 31811119 Free PMC article.
-
Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics.Heredity (Edinb). 2012 Jan;108(1):75-85. doi: 10.1038/hdy.2011.100. Epub 2011 Nov 16. Heredity (Edinb). 2012. PMID: 22086080 Free PMC article. Review.
-
Evaluation of the performance of copy number variant prediction tools for the detection of deletions from whole genome sequencing data.J Biomed Inform. 2019 Jun;94:103174. doi: 10.1016/j.jbi.2019.103174. Epub 2019 Apr 6. J Biomed Inform. 2019. PMID: 30965134 Review.
Cited by
-
HiFi long-read amplicon sequencing for full-spectrum variants of human mtDNA.BMC Genomics. 2024 May 31;25(1):538. doi: 10.1186/s12864-024-10433-9. BMC Genomics. 2024. PMID: 38822239 Free PMC article.
-
Genetic landscape of interval and screen detected breast cancer.NPJ Precis Oncol. 2024 May 28;8(1):122. doi: 10.1038/s41698-024-00618-6. NPJ Precis Oncol. 2024. PMID: 38806682 Free PMC article.
-
The evolution of lung adenocarcinoma precursors is associated with chromosomal instability and transition from innate to adaptive immune response/evasion.Res Sq [Preprint]. 2024 May 15:rs.3.rs-4396272. doi: 10.21203/rs.3.rs-4396272/v1. Res Sq. 2024. PMID: 38798564 Free PMC article. Preprint.
-
A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle.Genet Sel Evol. 2024 May 21;56(1):39. doi: 10.1186/s12711-024-00909-3. Genet Sel Evol. 2024. PMID: 38773368 Free PMC article.
-
The genomic landscape of Vk*MYC myeloma highlights shared pathways of transformation between mice and humans.Nat Commun. 2024 May 7;15(1):3844. doi: 10.1038/s41467-024-48091-w. Nat Commun. 2024. PMID: 38714690 Free PMC article.
References
-
- Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat Methods. 2009;6:S13–S20. - PubMed
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources