4.7 Article

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS

Journal

BIOINFORMATICS
Volume 28, Issue 5, Pages 619-627

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bts019

Keywords

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Funding

  1. European Union [241995]
  2. International Max Planck Research School for Computational Biology and Scientific Computing

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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 single-end 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. Availability: SplazerS is available from http://www.seqan.de/projects/splazers.

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