One of the QC steps I’ve started doing is that I now exclude indel LOFs from my analysis if they’re within 10bp of another indel in the same sample. I would love a way to do this filter step in Hail. I don’t think I currently can.
Edit: realized this was a genotype issue and not a variant issue. This would be like a filtergenotypes call, since I need to access sample information as well as variant information, but I also need to be able to compare genotypes to one another instead of strictly filtering based on one call’s properties.