How can I get "CHR" of every SNPs?

[Hisewetty]

No description provided.

[PerlineDemange]

Hi! I have the same problem using summary statistics which do not provide CHR:POS. I seem to understand from the tidy_inputGWAS function that this information is only required to remove the HLA region. If this is correct, would it be possible to make this optional? (I guess a work around is setting the CHR and POS to a location outside this region, or getting the CHR POS from one reference file)

[n-mounier]

Hello,
Indeed, this is used for removing the HLA region; but also for distance pruning (and for LD pruning if using the API, as this is done chromosome by chromosome, to make sure that the number of SNPs to prune at once is not too large). Now that there is an option to use plink to do this locally, I made sure that the chr:pos information is not required if not needed.
Note that this also means that the HLA region is not excluded by default anymore.