We are happy to announce VarFish Release v0.23.0. The key feature of this release is the export of Clinvar XML from user annotation data with very few clicks. This release also includes new external service integration and various bug fixes.
An important task in rare disease genetics variant analysis is the export to Clinvar. NCBI itself offers a web-based wizard and spreadsheet based templates for preparing submissions. However, filling these for many variants is a very tedious task.
Starting with its current release v0.23.0, VarFish allows to export variants into a Clinvar XML file suitable for submission with a few clicks.
VarFish already allows users to easily annotate variants based on flags, color codes, and ACMG variant assertion criteria. Also, individuals can be annotated with HPO terms as well as Orphanet and OMIM diseases. Once the analysis of a case is complete, the already curated information can be used to create a Clinvar XML submission file with few clicks. This removes the need to tediously and manually copy over the information that entered into one program such as VarFish into a second program such as Excel.
We asked ourselves: can we automate this even further? Sadly, NCBI Clinvar does not offer an API (application programming interface) such that you currently cannot create your submission directly from VarFish. The generated XML files have to be uploaded manually into Clinvar.
Internal Users
Are you are a Charite, BIH, or MDC researcher? Then you don’t have to run your own but can use our internal instance. Simply send us an email to cubi-helpdesk@bih-charite.de and let us discuss about a collaboration.
More About VarFish
You can read more about VarFish here:
- VarFish Homepage
- BIH press release New software detects disease-causing gene mutations
VarFish Publication
- Holtgrewe, M.; Stolpe, O.; Nieminen, M.; Mundlos, S.; Knaus, A.; Kornak, U.; Seelow, D.; Segebrecht, L.; Spielmann, M.; Fischer-Zirnsak, B.; Boschann, F.; Scholl, U.; Ehmke, N.; Beule, D. VarFish: Comprehensive DNA Variant Analysis for Diagnostics and Research. Nucleic Acids Research 2020, gkaa241. https://doi.org/10.1093/nar/gkaa241.
Last modified: Feb 7, 2023