RDNAcaller: a fast and robust pipeline to call ribosomal DNA variants.

ABSTRACT: Ribosomal DNA (rDNA) is arranged in tandem repeats in the human genome. Extensive genetic and copy number variation in rDNA has been reported both within and between individuals, contributing to phenotypic diversity. However, traditional variant callers, designed for diploid regions, have not been systematically benchmarked for analyzing rDNA. We developed a customized simulator that replicates real intra- and inter-individual rDNA variation to benchmark the performance of commonly used variant callers, including GATK, Mutect2, and Lofreq*. Additionally, we optimized the preprocessing and mapping steps to significantly improve accuracy. Based on these optimizations, we introduce rDNAcaller, a novel pipeline for accurate rDNA variant detection using short-read whole-genome sequencing

SUBMITTER: Ramirez JM 

PROVIDER: S-EPMC12714689 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature