Hi guys, where are we with this? I know a group in Germany that is quite interested on this topic and they have a cool tool to do variant prioritisation, I shared with them a link to join this channel but it would be good to check where everyone is with this at the moment so they have a better feel if this is the right group for them and if they want to switch their pipeline to nf-core style?

can you link the tool?

I think is this one: https://github.com/cio-abcd/variantinterpretation but I see that one of them already join and maybe they can correct me if I am wrong @Kai Horny. Thank you

Hi Raquel, yes this is the tool! For now its a simple pipeline that first does annotation and some postprocessing so that oncologist can work with the reports. 1. Filtering for the transcript or based on customizable filters. 2. conversion to TSV file and HTML report. 3. Calculating the TMB from the VCFs in different ways. We have several ideas in mind how to proceed with this workflow to add e.g. much more databases and keeping it very customizable for the users.

That sounds great to me already! Even more so if it is being used in the clinic. I myself was doing something similar in python a couple of years ago but it was only in-house use for a specific project.

Hi Kai, looks really cool, thanks for sharing! currently, you are based only on VEP, right? Do you follow the any guidelines (e.g. ACMG) for prioritization?

thanks, I also saw your pipeline in whcih you implemented CGI and CIVIC already, that also looks nice. Currently we did not implement a variant prioritization, but that would be a really nice addition. We focused on the customizable filters, so that the report can be reduced to smaller variant lists that can be checked by the molecular pathologists.