Detection of structural variants and indels within exome data

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

Research output: Contribution to journalArticle

77 Citations (Scopus)

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 2012
Externally publishedYes

Fingerprint

Exome
Pseudogenes
Base Pairing
Sensitivity and Specificity
Datasets

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology

Cite this

Karakoc, E., Alkan, C., O'Roak, B., Dennis, M. Y., Vives, L., Mark, K., ... 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

Detection of structural variants and indels within exome data. / Karakoc, Emre; Alkan, Can; O'Roak, Brian; Dennis, Megan Y.; Vives, Laura; Mark, Kenneth; Rieder, Mark J.; Nickerson, Debbie A.; Eichler, Evan E.

In: Nature Methods, Vol. 9, No. 2, 02.2012, p. 176-178.

Research output: Contribution to journalArticle

Karakoc, E, Alkan, C, O'Roak, B, Dennis, MY, Vives, L, Mark, K, Rieder, MJ, Nickerson, DA & Eichler, EE 2012, 'Detection of structural variants and indels within exome data', Nature Methods, vol. 9, no. 2, pp. 176-178. https://doi.org/10.1038/nmeth.1810
Karakoc E, Alkan C, O'Roak B, Dennis MY, Vives L, Mark K et al. Detection of structural variants and indels within exome data. Nature Methods. 2012 Feb;9(2):176-178. https://doi.org/10.1038/nmeth.1810
Karakoc, Emre ; Alkan, Can ; O'Roak, Brian ; Dennis, Megan Y. ; Vives, Laura ; Mark, Kenneth ; Rieder, Mark J. ; Nickerson, Debbie A. ; Eichler, Evan E. / Detection of structural variants and indels within exome data. In: Nature Methods. 2012 ; Vol. 9, No. 2. pp. 176-178.
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