Entering edit mode
4.3 years ago
vctrm67
▴
50
Is running Annovar in the hg19 build OK if my vcfs are produced using GRCh37? I can run it without errors but I am unsure of the quality of the annotations. Should I LiftOver to hg19 first instead?
I don't think that will be a problem, GRCh37 and hg19 are interchangeable in this context.
They have different chromosome naming conventions, don't they? I'm sure they have more differences but regardless, this is okay then?
Good point - you might need to account for the different chromosome names. I was only thinking about the coordinates and totally missed the chr names, sorry!