Name
Title | ||
|---|---|---|
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. |
Abstract | ||
|---|---|---|
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.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.SplazerS is available from http://www.seqan.de/projects/ splazers.Supplementary data are available at Bioinformatics online. |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1093/bioinformatics/bts019 | Bioinformatics |
Keywords | Field | DocType |
genomic resequencing data,supplementary data,single-and paired-end,alternative split mapping method,resequencing data,read-to-reference alignment,structural variation,genomic indel variant,genomic variation,alignment error,exact breakpoints,de supplementary information,targeted resequencing data,biological sciences,dna | Structural variation,Paired-end tag,Computer science,Breakpoint,Bioinformatics,Indel | Journal |
Volume | Issue | ISSN |
28 | 5 | 1367-4811 |
Citations | PageRank | References |
7 | 0.65 | 11 |
Authors | ||
8 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Anne-katrin Emde | 1 | 101 | 6.06 |
| Marcel H Schulz | 2 | 240 | 24.03 |
| David Weese | 3 | 252 | 17.79 |
| Ruping Sun | 4 | 8 | 1.39 |
| Martin Vingron | 5 | 1754 | 298.16 |
| Vera M Kalscheuer | 6 | 7 | 0.65 |
| Stefan A Haas | 7 | 47 | 4.48 |
| Knut Reinert | 8 | 1020 | 105.87 |