Journal
BIOINFORMATICS
Volume 30, Issue 8, Pages 1064-1072Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btt767
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Funding
- National Health and Medical Research Council (NHMRC) [637357]
- Victorian State Government Operational Infrastructure Support
- Australian Government NHMRC IRIISS
- Melbourne Melanoma Project
- Victorian Cancer Biobank
- Victorian Cancer Agency
- Cancer Council of Victoria scholarship
- NICTA
- Australian Government
- Department of Broadband, Communications and the Digital Economy
- Australian Research Council through the ICT Centre of Excellence program
- NHMRC Principal Research Fellowship
- Cancer Council Victoria
- Leukaemia Foundation of Australia
- Pfizer Australia
- VESKI
- NHMRC Career Development Fellowship [1003856]
- Lorenzo and Pamela Galli Melanoma Research Fellowship
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Motivation: Methods for detecting somatic genome rearrangements in tumours using next-generation sequencing are vital in cancer genomics. 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 significant computational burden and high false-positive or falsenegative rates. Results: In this article, we present Socrates (SOft Clip re-alignment To idEntify Structural variants), a highly efficient and effective method for detecting genomic rearrangements in tumours that uses only splitread data. Socrates has single-nucleotide resolution, identifies micro-homologies and untemplated sequence at break points, has high sensitivity and high specificity and takes advantage of parallelism for efficient use of resources. We demonstrate using simulated and real data that Socrates performs well compared with a number of existing structural variant detection tools.
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