Customize annotation of specific mutations #395
Description
It is known that specific synonymous mutations in genes can have a functional impact. It would be nice to be able to modify their annotation to something different from synonymous so that they are not used for building any background nor anything of this kind.
See this paragraph from the supplementary material of this paper:
Lawson, A.R.J., Abascal, F., Nicola, P.A. et al. Somatic mutation and selection at population scale. Nature 647, 411–420 (2025). https://doi.org/10.1038/s41586-025-09584-w
This would require some modifications to the current scripts for customizing annotation.