Abstract
Motivation: The reliable detection of genomic variation in resequencing data is still a major challenge, especially for variants larger than a few base pairs. Sequencing reads crossing boundaries of structural variation carry the potential for their identification, but are difficult to map. Results: Here we present a method for 'split' read mapping, where prefix and suffix match of a read may be interrupted by a longer gap in the read-to-reference alignment. We use this method to accurately detect medium-sized insertions and long deletions with precise breakpoints in genomic resequencing data. Compared with alternative split mapping methods, SplazerS significantly improves sensitivity for detecting large indel events, especially in variant-rich regions. Our method is robust in the presence of sequencing errors as well as alignment errors due to genomic mutations/divergence, and can be used on reads of variable lengths. Our analysis shows that SplazerS is a versatile tool applicable to unanchored or singleend as well as anchored paired-end reads. In addition, application of SplazerS to targeted resequencing data led to the interesting discovery of a complete, possibly functional gene retrocopy variant.
Original language | English (US) |
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Article number | bts019 |
Pages (from-to) | 619-627 |
Number of pages | 9 |
Journal | Bioinformatics |
Volume | 28 |
Issue number | 5 |
DOIs | |
State | Published - Mar 2012 |
Externally published | Yes |
Bibliographical note
Funding Information:Funding: European Union’s Seventh Framework Program under grant agreement number 241995, project GENCODYS; International Max Planck Research School for Computational Biology and Scientific Computing.