With the recognition of the need for reproducibility in the face of increasing data complexity, we implemented a series of metrics and an interactive visualization prototype to facilitate discovery and interpretation for next generation sequencing use cases: copy number variant detection with exome sequencing and chromatin immunoprecipitation followed by sequencing (ChIP-seq). This interactive framework is an important first step to provide measurable and consistent check of data validity for each step of the analysis. The goal is to allow scientists to assess the validity of their methods, ensure the accuracy of the data and guide prioritization by obtaining high confidence findings. It is important to note that the interactive component allows identification of issues or characteristics of the data that would have been missed in traditional static plots. We note this is an iterative process and with further evaluation and testing, additional metrics and contextual views can be added.