Obtain equivalent variant ids (chr-pos-ref-alt) for GRCh37 and GRCh38

Question

[fla28]

Hi all,

I want to obtain the equivalent variant id (chr-pos-ref-alt) from GRCh38 in GRCh37. This is to deal with some variants poorly lifted over.

To exemplify, see the variant https://gnomad.broadinstitute.org/variant/10-17838942-A-G?dataset=gnomad_r3

It has two equivalents in GRCh37.

I want to submit a list of GRCh38 variants, and get a list (array) of equvalent GRCh37 variants.

Does anyone know of a tool that provides that?

Thanks a lot in advance!

[iraun]

Liftovering is the way of converting the coordinates from one assembly to another. Not sure if you have done this already since you mentioned "some variants poorly lifted over"? Here you can find a nice overview of tools for liftovering.

[fla28]

Yes, I have already lifted the variants from GRCh37 to GRCh38. Now I am selecting the duplicated variants generated in this process and tracing back to the original variant to select which one to keep (each one of the duplicates have a different weight). Is it clearer now? Thank you anyway, iraun!