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Bioinformatics. 2012 Mar 1;28(5):619-27. doi: 10.1093/bioinformatics/bts019. Epub 2012 Jan 11.

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

Author information

1
Department of Computer Science, Freie Universit├Ąt Berlin, Takustrasse 9, Max-Planck-Institute for Molecular Genetics, Berlin, Germany. emde@inf.fu-berlin.de

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 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.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
22238266
DOI:
10.1093/bioinformatics/bts019
[Indexed for MEDLINE]

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