Difference between genomic build annotations

Question

[filippo]

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

Answer 1

[JC]

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