sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies

Abstract

Motivation: Retrocopies or processed pseudogenes are gene copies resulting from mRNA retrotransposition. These gene duplicates can be fixed, somatically inserted or polymorphic in the genome. However, knowledge regarding unfixed retrocopies (retroCNVs) is still limited, and the development of computational tools for effectively identifying and genotyping them is an urgent need. Results: Here, we present sideRETRO, a pipeline dedicated not only to detecting retroCNVs in whole-genome or whole-exome sequencing data but also to revealing their insertion sites, zygosity and genomic context and classifying them as somatic or polymorphic events. We show that sideRETRO can identify novel retroCNVs and genotype them, in addition to finding polymorphic retroCNVs in whole-genome and whole-exome data. Therefore, sideRETRO fills a gap in the literature and presents an efficient and straightforward algorithm to accelerate the study of bona fide retroCNVs.