This workflow is a critical component in generating scoring metrics needed to classify pathogenicity of variants. The workflow has three processing steps:
- Strip VCF input of old annotations. This is done in order to dramatically reduce resource usage of ANNOVAR, which does not require pre-existing annotations
- Run ANNOVAR latest (software has no versioning, only references) to gather needed scoring metrics
- Run InterVar v2.2.1
In addition, file compression steps are run to reduce output size.