Variant Browser is under active development with features being added successively. For any suggestions or bug reports, please contact our support team at [email protected].
Variant Browser is an application for genome analysis and interpretation that will allow researchers and clinicians to quickly annotate and accurately prioritize variants and genes involved in a disease. Variant Browser bridges the gap between sequencing/raw data management and clinical management, providing robust genome interpretation to expedite diagnosis and accelerate the understanding of the genetic basis of disease, drug response, and health.
During the BETA stage, you are able to interpret demo VCF files which are readily available inside the app. The available options include filtering with configurable filtering criteria, directly opening the Genome Browser at the position of the selected variant and displaying general statistics for the currently applied filters. In case you want to interpret your own VCF files please contact us at [email protected].
Future development will include an integrated flow for annotation and interpretation of VCF files using the Variant Browser, with annotated files provided by annotation apps on Cavatica (such as VEP annotation workflow or SnpEff), or uploaded by the users. Additionally, there will be more detailed and elaborate filtering options, along with more comprehensive display options for relevant analysis information.
Try the Variant Browser right now by accessing it in your project's Interactive Analysis section and read more about it in the documentation.
Several resources that will be used for creation of sqlite databases to be browsed further with Variant Browser are already available on Cavatica. Those are annotation workflows based on VEP (Variant Effect Predictor) and SnpEff. Workflows for annotation and conversion of a single VCF file to an sqlite database are: VEP annotation & DB conversion and SnpEff annotation & DB conversion, as well as Trios: SnpEff annotation & DB conversion or Trios: VEP annotation & DB conversion in case of Trios analysis. The workflows are available in the Variant Browser public project.