Is anyone using CADD 1.6.1 with "chr1" style chromosome names successfully? It seems like it should be supported based on the documentation, but I just have to apply various ugly hacks.. This line in particular, I can't see how it could work... https://github.com/kircherlab/CADD-scripts/blob/1fead0c1e02d3f0a8599bdb04e6b3a2dd70b4866/src/scripts/annotateVEPvcf.py#L112

I have not gotten it to work, had to rename from reference to "1"-style and then back to reference. Maybe this is something the CADD team would fix? Otherwise I've updated the annotate_cadd subworkflow with the renaming processes, and perhaps the same could be done in raredisease: https://github.com/genomic-medicine-sweden/nallo/blob/dev/subworkflows/local/annotate_cadd/main.nf

Ok it's great to have it in the nallo pipeline, and I think it makes sense to add it like this to raredisease as well. We will also have to consider updating to CADD 1.7, but I think it's difficult to get running