Annovar in hg19 mode

Question

[vctrm67]

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?

[Ram]

I don't think that will be a problem, GRCh37 and hg19 are interchangeable in this context.

[vctrm67]

They have different chromosome naming conventions, don't they? I'm sure they have more differences but regardless, this is okay then?

[Ram]

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!

Answer 1

[Kevin Blighe]

The Broad Institute did some low-level comparisons between the different versions of that release of the human genome and found no differences between hg19 and GRCh37 on chr1-24: GRCh37 / hg19 / b37 / humanG1Kv37 - Human Reference Discrepancies

So, you do not need to worry.