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Detection of structural variants and indels within exome data.

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.

SUBMITTER: Karakoc E

PROVIDER: S-EPMC3269549 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature

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Detection of structural variants and indels within exome data.

Karakoc Emre E Alkan Can C O'Roak Brian J BJ Dennis Megan Y MY Vives Laura L Mark Kenneth K Rieder Mark J MJ Nickerson Debbie A DA Eichler Evan E EE

Nature methods 20111218 2

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. ...[more]

PMID: 22179552

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