Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Emde, A., Schulz, M. H., Weese, D., Sun, R., Vingron, M., Kalscheuer, V. M., Haas, S. A., & Reinert, K. Bioinformatics (Oxford, England), 28(5):619–627, March, 2012.
doi  abstract   bibtex   
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.
@article{emde_detecting_2012,
	title = {Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using {SplazerS}},
	volume = {28},
	issn = {1367-4811},
	doi = {10.1093/bioinformatics/bts019},
	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.},
	language = {eng},
	number = {5},
	journal = {Bioinformatics (Oxford, England)},
	author = {Emde, Anne-Katrin and Schulz, Marcel H. and Weese, David and Sun, Ruping and Vingron, Martin and Kalscheuer, Vera M. and Haas, Stefan A. and Reinert, Knut},
	month = mar,
	year = {2012},
	pmid = {22238266},
	keywords = {Algorithms, Genomics, Humans, INDEL Mutation, Sequence Analysis, DNA},
	pages = {619--627},
	file = {Volltext:/Users/mschulz/Zotero/storage/45JYHFG2/Emde et al. - 2012 - Detecting genomic indel variants with exact breakp.pdf:application/pdf},
}

Downloads: 0