Shiny-SoSV: A web-based performance calculator for somatic structural variant detection.

ABSTRACT: Somatic structural variants are an important contributor to cancer development and evolution. Accurate detection of these complex variants from whole genome sequencing data is influenced by a multitude of parameters. However, there are currently no tools for guiding study design nor are there applications that could predict the performance of somatic structural variant detection. To address this gap, we developed Shiny-SoSV, a user-friendly web-based calculator for determining the impact of common variables on the sensitivity, precision and F1 score of somatic structural variant detection, including choice of variant detection tool, sequencing depth of coverage, variant allele fraction, and variant breakpoint resolution. Using simulation studies, we determined singular and combinatoric eff

SUBMITTER: Gong T 

PROVIDER: S-EPMC7451576 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature