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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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© The Authors 2012
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 Urheber:
Emde, Anne Katrin1, Autor
Schulz, Marcel H.2, Autor
Weese, David1, Autor
Sun, Ruping3, Autor           
Vingron, Martin4, Autor           
Kalscheuer, Vera M.5, Autor           
Haas, Stefan3, Autor           
Reinert, Knut1, Autor
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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Schlagwörter: Algorithms Genomics/ methods Humans INDEL Mutation Sequence Analysis, DNA
 Zusammenfassung: 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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Sprache(n): eng - English
 Datum: 2012-01-112012
 Publikationsstatus: Erschienen
 Seiten: -
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: DOI: 10.1093/bioinformatics/bts019
 Art des Abschluß: -

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Titel: Bioinformatics
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: Oxford : Oxford University Press
Seiten: - Band / Heft: 28 (5) Artikelnummer: - Start- / Endseite: 619 - 27 Identifikator: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991