A comprehensive review of deep learning-based variant calling methods

Abstract

Genome sequencing data have become increasingly important in the field of personalized medicine and diagnosis. However, accurately detecting genomic variations remains a challenging task. Traditional variation detection methods rely on manual inspection or predefined rules, which can be time-consuming and prone to errors. Consequently, deep learning-based approaches for variation detection have gained attention due to their ability to automatically learn genomic features that distinguish between variants. In our review, we discuss the recent advancements in deep learning-based algorithms for detecting small variations and structural variations in genomic data, as well as their advantages and limitations.

Keywords: SNP and Indel; deep learning; genomic variation; structural variation; variant calling.