ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.

ABSTRACT: Comprehensive identification of insertions/deletions (indels) across the full size spectrum from second generation sequencing is challenging due to the relatively short read length inherent in the technology. Different indel calling methods exist but are limited in detection to specific sizes with varying accuracy and resolution. We present ScanIndel, an integrated framework for detecting indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, we demonstrate ScanIndel's superior sensitivity and specificity relative to several state-of-the-art indel callers across various coverage levels and indel sizes. ScanIndel yields higher predictive accuracy with lower computational cost compared with existing tools for both targeted reseque

SUBMITTER: Yang R 

PROVIDER: S-EPMC4671222 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature