Detection of structural variants and indels within exome data
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Updated: May 26, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Emre Karakoc1, Can Alkan, Brian J O'Roak
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
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.
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