Detection of structural variants and indels within exome data

Emre Karakoc, Can Alkan, Brian J. O'Roak, Megan Dennis, Laura Vives, Kenneth Mark, Mark J. Rieder, Debbie A. Nickerson, Evan E. Eichler

Research output: Contribution to journalArticle

78 Scopus citations

Abstract

We report an algorithm to detect structural variation and indels from 1 base pair (bp) to 1 Mbp within exome sequence data sets. Splitread uses one end-anchored placements to cluster the mappings of subsequences of unanchored ends to identify the size, content and location of variants with high specificity and sensitivity. The algorithm discovers indels, structural variants, de novo events and copy number-polymorphic processed pseudogenes missed by other methods.

Original languageEnglish (US)
Pages (from-to)176-178
Number of pages3
JournalNature Methods
Volume9
Issue number2
DOIs
StatePublished - Feb 1 2012
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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  • Cite this

    Karakoc, E., Alkan, C., O'Roak, B. J., Dennis, M., Vives, L., Mark, K., Rieder, M. J., Nickerson, D. A., & Eichler, E. E. (2012). Detection of structural variants and indels within exome data. Nature Methods, 9(2), 176-178. https://doi.org/10.1038/nmeth.1810