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Difference between genomic build annotations

Hi everyone.

I have a question regarding annotating genomic builds.

I have annotated ~800k markers in hg19 with ANNOVAR with basically all the databases available (which is quite time consuming). I have now been asked to annotate the same 800k markers with hg38. I am not sure which of the following strategy is best:

  • Use the current annotated hg19 markers and simply do a liftover
  • Re-do the entire process from hg38 -> do a liftover of my current markers to hg38 and then run ANNOVAR again

Not sure if it makes a difference. Thinking about do a liftover of already annotated markers as it is 1) easier and 2) there are more datasets for annotation in hg19 compared to hg38.

Thanks! Filippo

snp genome snp gene
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updated by JC JC • written by filippo • filippo

1 answer

Option 1 is better, you are right about option 2, there are fewer annotations for hg38

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written by JC JC

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