Socrates: Identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads
- Author(s)
- Schroder, J; Hsu, A; Boyle, SE; Macintyre, G; Cmero, M; Tothill, RW; Johnstone, RW; Shackleton, M; Papenfuss, AT;
- Journal Title
- Bioinformatics
- Abstract
- Motivation Methods for detecting somatic genome rearrangements in tumours using next generation sequencing are vital in cancer geno- mics. Available algorithms use one or more sources of evidence, such as read depth, paired end reads or split reads to predict structural variants. However, the problem remains challenging due to the signi- ficant computational burden, and high false positive or false negative rates. Results In this paper we present Socrates, a highly efficient and effective method for detecting genomic rearrangements in tumours that utilises only split-read data. Socrates has single nucleotide reso- lution, identifies micro-homologies and untemplated sequence at breakpoints, has very high sensitivity and high specificity, and takes advantage of parallelism for efficient use of resources. We demon- strate using simulated and real data that Socrates performs well compared to a number of existing SV detection tools.
- Publisher
- Oxford Press
- Research Division(s)
- Bioinformatics
- Publisher's Version
- https://doi.org/10.1093/bioinformatics/btt767
- Open Access at Publisher's Site
http://bioinformatics.oxfordjournals.org/content/early/2014/01/22/bioinformatics.btt767.long- Terms of Use/Rights Notice
- © The Author 2014. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Creation Date: 2014-01-21 10:45:18