Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools.

ABSTRACT: The next-generation sequencing (NGS) technology represents a significant advance in genomics and medical diagnosis. Nevertheless, the time it takes to perform sequencing, data analysis, and variant interpretation is a bottleneck in using next-generation sequencing in precision medicine. For accurate and efficient performance in clinical diagnostic lab practice, a consistent data analysis pipeline is necessary to avoid false variant calls and achieve optimum accuracy. This study aims to compare the performance of two NGS data analysis pipeline compartments, including short-read mapping (BWA-MEM and BWA-MEM2) and variant calling (GATK-HaplotypeCaller and DRAGEN-GATK). On Whole Exome Sequencing (WES) data, computational performance was assessed using several criteria, including mapping effici

SUBMITTER: Alganmi N 

PROVIDER: S-EPMC10399881 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature