Combining callers improves the detection of copy number variants from whole-genome sequencing.

ABSTRACT: Copy Number Variants (CNVs) are deletions, duplications or insertions larger than 50 base pairs. They account for a large percentage of the normal genome variation and play major roles in human pathology. While array-based approaches have long been used to detect them in clinical practice, whole-genome sequencing (WGS) bears the promise to allow concomitant exploration of CNVs and smaller variants. However, accurately calling CNVs from WGS remains a difficult computational task, for which a consensus is still lacking. In this paper, we explore practical calling options to reach the best compromise between sensitivity and sensibility. We show that callers based on different signal (paired-end reads, split reads, coverage depth) yield complementary results. We suggest approaches combining fo

SUBMITTER: Coutelier M 

PROVIDER: S-EPMC8821561 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature