sideRETRO

sideRETRO detects and genotypes somatic and dimorphic insertions of processed pseudogenes (retrocopies/retroCNVs) from whole-genome (WGS) and whole-exome (WES) sequencing data and identifies their genomic insertion sites to support zygosity and contextual analyses.

Key Features:

• Detection of RetroCNVs: Identifies novel retrocopies/retroCNVs in WGS and WES datasets, including somatic insertions and dimorphic events between individuals.
• Genotyping Accuracy: Determines zygosity (homozygous or heterozygous) of detected retroCNVs with a reported genotyping accuracy of 93.2%.
• Insertion Site Identification: Pinpoints exact genomic insertion sites of processed pseudogene retrotransposition events.
• Classification of Events: Classifies detected retroCNVs as somatic or dimorphic to distinguish population variation from somatic occurrences.
• Efficient Algorithm: Employs an algorithm optimized for rapid identification and classification of retroCNVs in large genomic datasets.

Scientific Applications:

• Genomic Research: Enables identification and characterization of retroCNVs to investigate genetic diversity and evolutionary processes.
• Disease Studies: Detects somatic retroCNVs relevant to cancer research and studies of somatic mutation contributions to disease.
• Genetic Variation Analysis: Facilitates analysis of dimorphic retroCNVs to assess population-level genetic variation.

Methodology:

Implemented in C, sideRETRO uses HTSlib for SAM/BAM/CRAM file handling and SQLite3 for data management and analysis.