Annovar in hg19 mode
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22 months ago
vctrm67 ▴ 20

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

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

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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!

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22 months ago

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.

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