{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T18:10:35Z","timestamp":1772129435555,"version":"3.50.1"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Results: Here we present a method for \u2018split\u2019 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.<\/jats:p>\n               <jats:p>Availability: SplazerS is available from http:\/\/www.seqan.de\/projects\/ splazers.<\/jats:p>\n               <jats:p>Contact: \u00a0emde@inf.fu-berlin.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts019","type":"journal-article","created":{"date-parts":[[2012,1,12]],"date-time":"2012-01-12T03:10:30Z","timestamp":1326337830000},"page":"619-627","source":"Crossref","is-referenced-by-count":66,"title":["Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS"],"prefix":"10.1093","volume":"28","author":[{"given":"Anne-Katrin","family":"Emde","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, Takustrasse 9, 2Max-Planck-Institute for Molecular Genetics, Berlin, Germany, Ihnestrasse 63-73, 14195 Berlin, Germany and 3Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Complex, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA"},{"name":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, Takustrasse 9, 2Max-Planck-Institute for Molecular Genetics, Berlin, Germany, Ihnestrasse 63-73, 14195 Berlin, Germany and 3Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Complex, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA"}]},{"given":"Marcel H.","family":"Schulz","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, Takustrasse 9, 2Max-Planck-Institute for Molecular Genetics, Berlin, Germany, Ihnestrasse 63-73, 14195 Berlin, Germany and 3Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Complex, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA"}]},{"given":"David","family":"Weese","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, Takustrasse 9, 2Max-Planck-Institute for Molecular Genetics, Berlin, Germany, Ihnestrasse 63-73, 14195 Berlin, Germany and 3Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Complex, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA"}]},{"given":"Ruping","family":"Sun","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, Takustrasse 9, 2Max-Planck-Institute for Molecular Genetics, Berlin, Germany, Ihnestrasse 63-73, 14195 Berlin, Germany and 3Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Complex, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA"}]},{"given":"Martin","family":"Vingron","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, Takustrasse 9, 2Max-Planck-Institute for Molecular Genetics, Berlin, Germany, Ihnestrasse 63-73, 14195 Berlin, Germany and 3Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Complex, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA"}]},{"given":"Vera M.","family":"Kalscheuer","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, Takustrasse 9, 2Max-Planck-Institute for Molecular Genetics, Berlin, Germany, Ihnestrasse 63-73, 14195 Berlin, Germany and 3Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Complex, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA"}]},{"given":"Stefan A.","family":"Haas","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, Takustrasse 9, 2Max-Planck-Institute for Molecular Genetics, Berlin, Germany, Ihnestrasse 63-73, 14195 Berlin, Germany and 3Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Complex, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA"}]},{"given":"Knut","family":"Reinert","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, Takustrasse 9, 2Max-Planck-Institute for Molecular Genetics, Berlin, Germany, Ihnestrasse 63-73, 14195 Berlin, Germany and 3Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Complex, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,1,11]]},"reference":[{"key":"2023012512192036300_B1","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1101\/gr.112326.110","article-title":"Dindel: accurate indel calls from 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