Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery.

ABSTRACT:

Background

Accurate variant detection in the coding regions of the human genome is a key requirement for molecular diagnostics of Mendelian disorders. Efficiency of variant discovery from next-generation sequencing (NGS) data depends on multiple factors, including reproducible coverage biases of NGS methods and the performance of read alignment and variant calling software. Although variant caller benchmarks are published constantly, no previous publications have leveraged the full extent of available gold standard whole-genome (WGS) and whole-exome (WES) sequencing datasets.

Results

In this work, we systematically evaluated the performance of 4 popular short read aligners (Bowtie2, BWA, Isaac, and Novoalign) and 9 novel and well-established variant calling and filtering met

SUBMITTER: Barbitoff YA 

PROVIDER: S-EPMC8862519 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature