Set-theory based benchmarking of three different variant callers for targeted sequencing.

ABSTRACT:

Background

Next generation sequencing (NGS) technologies have improved the study of hereditary diseases. Since the evaluation of bioinformatics pipelines is not straightforward, NGS demands effective strategies to analyze data that is of paramount relevance for decision making under a clinical scenario. According to the benchmarking framework of the Global Alliance for Genomics and Health (GA4GH), we implemented a new simple and user-friendly set-theory based method to assess variant callers using a gold standard variant set and high confidence regions. As model, we used TruSight Cardio kit sequencing data of the reference genome NA12878. This targeted sequencing kit is used to identify variants in key genes related to Inherited Cardiac Conditions (ICCs), a group of cardiovascular

SUBMITTER: Molina-Mora JA 

PROVIDER: S-EPMC7791862 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature