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

Emde, A. K., Schulz, M. H., Weese, D., Sun, R., Vingron, M., Kalscheuer, V. M., et al. (2012). Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics, 28(5), 619-27. doi:10.1093/bioinformatics/bts019.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E882-C Version Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E883-A
Genre: Journal Article

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 Creators:
Emde, Anne Katrin1, Author
Schulz, Marcel H.2, Author
Weese, David1, Author
Sun, Ruping3, Author              
Vingron, Martin4, Author              
Kalscheuer, Vera M.5, Author              
Haas, Stefan3, Author              
Reinert, Knut1, Author
Affiliations:
1Department of Computer Science, Freie Universität Berlin, Berlin, Germany, ou_persistent22              
2Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Complex, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA , ou_persistent22              
3Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Germany, ou_1479640              
4Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Germany, ou_1479639              
5Chromosome Rearrangements and Disease (Vera Kalscheuer), Dept. of Human Molecular Genetics (Head: Hans-Hilger Ropers), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Germany, ou_1479642              

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Free keywords: Algorithms Genomics/ methods Humans INDEL Mutation Sequence Analysis, DNA
 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.

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Language(s): eng - English
 Dates: 2012-01-112012
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1093/bioinformatics/bts019
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 28 (5) Sequence Number: - Start / End Page: 619 - 27 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991