pgenlibr: get chromosome and position for idx

[niekverw]

I was wondering if it's possible to obtain the chromosome and position by idx using pgenlibr, or if it is possible to add this feature?

Thanks so much. The pgenlibr is really useful for an R user like me.

[chrchang]

This isn't currently built-in, but if you use plink2 --set-all-var-ids on your dataset first, it's straightforward to extract chrom/pos from the ID strings.

[niekverw]

Thanks for your answer! I understand, but I actually need the ID's to be as they are, since they can be genes or other variants that are not captured by the position/variants alone.

[chrchang]

You can use --recover-var-ids to recover the original IDs whenever they're needed.