unCOVERApp: an interactive graphical application for clinical assessment of sequence coverage at the base-pair level

Motivation Next Generation Sequencing (NGS) is increasingly adopted in the clinical practice largely thanks to concurrent advancements in bioinformatic tools for variant detection and annotation. Despite improvements in available approaches, the need to assess sequencing quality down to the base-pair level still poses challenges for diagnostic accuracy. One of the most popular quality parameters of diagnostic NGS is the percentage of targeted bases characterized by low depth of coverage (DoC). These regions potentially hide a clinically-relevant variant, but no annotation is usually returned for them. However, visualizing low-DoC data with their potential functional and clinical consequences may be useful to prioritize inspection of specific regions before re-sequencing all coverage gaps or making assertions about completeness of the diagnostic test. To meet this need we have developed unCOVERApp, an interactive application for graphical inspection and clinical annotation of low-DoC genomic regions containing genes. Results unCOVERApp is a suite of graphical and statistical tools to support clinical assessment of low-DoC regions. Its interactive plots allow to display gene sequence coverage down to the base-pair level, and functional and clinical annotations of sites below a user-defined DoC threshold can be downloaded in a user-friendly spreadsheet format. Moreover, unCOVERApp provides a simple statistical framework to evaluate if DoC is sufficient for the detection of somatic variants, where the usual 20x DoC threshold used for germline variants is not adequate. A maximum credible allele frequency calculator is also available allowing users to set allele frequency cut-offs based on assumptions about the genetic architecture of the disease instead of applying a general one (e.g. 5%). In conclusion, unCOVERApp is an original tool designed to identify sites of potential clinical interest that may be hidden in diagnostic sequencing data. Availability unCOVERApp is a freely available application written in R and developed with Shiny packages and available in GitHub.