cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing

Abstract

cgpPindel is a modified version of Pindel that is optimized for detecting somatic insertions and deletions (indels) in cancer genomes and other samples compared to a reference control. Post-hoc filters remove false positive calls, resulting in a high-quality dataset for downstream analysis. This unit provides concise instructions for both a simple 'one-shot' execution of cgpPindel and a more detailed approach suitable for large-scale compute farms.

Keywords: Pindel; cancer; sequencing; somatic.