Find rsids from <chr:pos>

Hail Query & hailctl
1

Hi all,

In my MatrixTable, the “rsid” column does not contain the rsids (e.g. rs3431231), instead its content is saved similar to the locus key, as “chr:pos:a1:a2” (e.g. “21:14338253:T:C”). Is there a way to get the rsids corresponding to each variant’s position based on a reference panel?

Thanks a lot!
Kaveh

2

I think the easiest way to get the rsid is by either:

  1. Annotating with VEP (I believe one of the id fields in VEP annotation ought to be the rsid). See: https://hail.is/docs/0.2/methods/genetics.html#hail.methods.vep
  2. Using the annotation database to annotate with dbsnp. See: https://hail.is/docs/0.2/annotation_database_ui.html

Either way, you have to pull in some outside annotation source that knows about rsids.

1 Like
3

Hi John,

Thanks a lot for responding!
How would I annotate with dbSNP? The reason for asking is that I don’t see dbSNP in the list of available databases.

4

@kkarbasi did you ever find a solution to this using the dbSNP? I’ve been banging my head against this for awhile.