Local variant annotation and interpretation search for pathologists
- Install all requirements in a local python environment with pip.
- Create a CSV with variant annotations listed per line which should contain the following columns:
- chr: chromosome (free text)
- pos: genomic coordinate (int)
- ref: reference annotation (free text)
- alt: variant annotation (free text)
- classification: One of the following: "Not set", "Pathogenic", "Likely Pathogenic"
- somatic: One of the following: "Not set", "Somatic", "Not Confirmed Somatic", "Germline", "Artifact"
- curation: Free text of the variant interpretation
- enterDate: The date that the variant was entered, in YYYY-MM-DD HH:MM:SS format (e.g. 2023-06-21 11:29:01)
- Load this file into the window that appears, and search for something