hello everyone, I got a vcf file with variation called using hg38 as reference genome. I wonder what would happen if I use hg19 as reference genome to annotate these variants. Would it be OK or get wrong?
Alignment, variation-calling, and annotation should always be performed on the exact same reference. Not a similar one. If you want to use a different reference, start anew from alignment. It's also possible to use LiftOver but you'll get a different answer.