VarAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data.

ABSTRACT:

Motivation

Computational identification of copy number variants (CNVs) in sequencing data is a challenging task. Existing CNV-detection methods account for various sources of variation and perform different normalization strategies. However, their applicability and predictions are restricted to specific enrichment protocols. Here, we introduce a novel tool named varAmpliCNV, specifically designed for CNV-detection in amplicon-based targeted resequencing data (Haloplex™ enrichment protocol) in the absence of matched controls. VarAmpliCNV utilizes principal component analysis (PCA) and/or metric dimensional scaling (MDS) to control variances of amplicon associated read counts enabling effective detection of CNV signals.

Results

Performance of VarAmpliCNV was compared against t

SUBMITTER: Kumar AA 

PROVIDER: S-EPMC9805572 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature