Detection of structural variants and indels within exome data

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

Research output: Contribution to journalArticlepeer-review

87 Scopus citations


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
Issue number2
StatePublished - Feb 2012
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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