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sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies
- Source :
- Bioinformatics. 37:419-421
- Publication Year :
- 2020
- Publisher :
- Oxford University Press (OUP), 2020.
-
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. Availability and implementation sideRETRO is available at https://github.com/galantelab/sideRETRO Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects :
- Statistics and Probability
Genotype
Somatic cell
Pseudogene
Retrotransposon
Context (language use)
Computational biology
Biology
Biochemistry
Genome
03 medical and health sciences
0302 clinical medicine
Exome
Molecular Biology
Genotyping
Gene
030304 developmental biology
0303 health sciences
Base Sequence
Genomics
Pipeline (software)
Computer Science Applications
Computational Mathematics
Computational Theory and Mathematics
030220 oncology & carcinogenesis
Pseudogenes
Software
Subjects
Details
- ISSN :
- 13674811 and 13674803
- Volume :
- 37
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....d332fbd838b8ff304106c6917da60e7c