Question: Annovar in hg19 mode
0
gravatar for vctrm67
9 months ago by
vctrm6710
vctrm6710 wrote:

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?

annovar • 279 views
ADD COMMENTlink written 9 months ago by vctrm6710

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

ADD REPLYlink written 9 months ago by RamRS30k

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

ADD REPLYlink written 9 months ago by vctrm6710

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!

ADD REPLYlink written 9 months ago by RamRS30k
0
gravatar for Kevin Blighe
9 months ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

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.

ADD COMMENTlink modified 9 months ago • written 9 months ago by Kevin Blighe65k
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