I have a VCF file and realized that one individual is an outlier and is often different than the others. I'd like to remove this individual and have the ALT and REF columns follow suit. For example, if only this removed individual had the ALT allele the ALT column would then have a "." in it instead of the ALT allele that is no longer present in the remaining samples. And same with indels.
I have tried this with VCFtools and VCFlib, but both do not recode the ALT and REF columns. Does anyone know of a tool that can do this without having to remake the entire VCF file?