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

doi:10.1038/nmeth.1810

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 journal › Article › peer-review

91 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 language	English (US)
Pages (from-to)	176-178
Number of pages	3
Journal	Nature Methods
Volume	9
Issue number	2
DOIs	https://doi.org/10.1038/nmeth.1810
State	Published - Feb 2012
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/nmeth.1810

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AU - Vives, Laura

AU - Mark, Kenneth

AU - Rieder, Mark J.

AU - Nickerson, Debbie A.

AU - Eichler, Evan E.

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Detection of structural variants and indels within exome data

Abstract

ASJC Scopus subject areas

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