A new tool CovReport generates easy-to-understand sequencing coverage summary for diagnostic reports

Abstract

in order to properly interpret the results of a diagnostic gene panel sequencing test, gene coverage needs to be taken into consideration. if coverage is too low, an additional re-sequencing test is needed to make sure that a pathogenic variant is not missed. to facilitate the interpretation of coverage data, we designed covReport, a novel easy-to-use visualization tool. covReport generates a concise coverage summary that allows one-glance assessment of the sequencing test performance. Both gene-level and exon-level coverage can be immediately appreciated and taken into consideration for further medical decisions. covReport does not require complex installation and can thus be easily implemented in any diagnostic laboratory setting. A user-friendly interface generates a graphic summary of coverage that can be directly included in the diagnostic report. in addition to a stand-alone version, we also provide a command line version of covReport that can be integrated into any bioinformatics pipeline. this flexible tool is now part of routine sequencing analysis at the Department of Medical Genetics at La timone Hospital (Marseille, france). covReport is available at http://jdotsoft.com/covReport.php. it is implemented in Java and supported on Windows, Mac oS X and Linux.