Missing rsIDs

[Dhanya Ramachandran]

Hi,

What happens when in an input file some rsIDs are missing, but the chr:pos:A1 columns are available? Does FUMA accept this or should I remove any rows with missing values?

Secondly, what is the range of exclusion (in basepair positions) for the MHC  locus? (only the extended one is defined in the tutorial)

Thanks a lot,

Dhanya

[d.p.wi...@vu.nl]

Hi Dhanya,

I checked the scenario which you outlined, I replaced the rsID with NA for one of the snps. This will cause the magma analysis to fail and snps with NA for an rsID will not be included in the manhattan plot. However this variant was included in the results table. Unfortunately, I think that different missing values will be treated differently so predicting the outcome is difficult. I recommend removing the rsID column if you have chr, bp, and alelle columns.

The MHC region is defined as  6:29624758-33170276.

Cheers,

Doug