Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays.

ABSTRACT:

Background

Benchmarking the performance of complex analytical pipelines is an essential part of developing Lab Developed Tests (LDT). Reference samples and benchmark calls published by Genome in a Bottle (GIAB) consortium have enabled the evaluation of analytical methods. The performance of such methods is not uniform across the different genomic regions of interest and variant types. Several benchmarking methods such as hap.py, vcfeval, and vcflib are available to assess the analytical performance characteristics of variant calling algorithms. However, assessing the performance characteristics of an overall LDT assay still requires stringing together several such methods and experienced bioinformaticians to interpret the results. In addition, these methods are dependent on the har

SUBMITTER: Krishnan V 

PROVIDER: S-EPMC7903625 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature