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bioRxiv · 10.1101/2021.12.16.473078

eXNVerify: coverage analysis for long and short-read sequencing data in clinical context

Porebski, S.·Stokowy, T.
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Abstract

Accurate identification of genetic variants to a large extent is based on type of experimental technology, quality of the material and coverage of obtained sequencing data. Our motivation was to create a tool that will evaluate genome coverage and accelerate the introduction of long-read sequencing to medical diagnostics and clinical practice. Here we present eXNVerify: a tool for inspection of clinical data in the context of pathogenic variants. The tool calculates Clinical Depth Coverage - a measure of coverage which we introduce to evaluate loci with pathogenic germline and somatic variants reported in ClinVar. The tool additionally provides visualization options for user-defined genes of interest. Finally, we present an examples of BRCA1, TP53, CFTR application and results of a test conducted in the Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development. eXNVerify is available at https://github.com/porebskis/eXNVerify and can be directly pulled from the DockerHub repository: docker pull porebskis/exnverify:1.0.

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Porebski, S., Stokowy, T.. 2021-12-17. eXNVerify: coverage analysis for long and short-read sequencing data in clinical context. https://doi.org/10.1101/2021.12.16.473078

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