PLINK --bmerge log file: Warning: Variants have the the same position

Question

[yy237]

Hi,

I am new to GWAS and PLINK in general so I am not really sure about what to do in the following:

After merging two sets of binary plink files using --bmerge, I see the following Warning message in my log file:

Warning: Variants 'rs1801131' and 'VG01S2022' have the same position. In total, I have 3 of those warning messages (total of 3 pairs of variants).

I tried searching and found both rs1801131 and VG01S2022 in my original two binary bim files (before merging), and the output merged bim file.

The merge went smoothly, but I am worried about whether this would affect downstream analyses. Is this something to worry about, and is there anything I should do before I proceed to the quality control steps?

Thank you very much!

Answer 1

[chrchang523]

Check if they have the same alleles. If they do, you probably want to merge the pair of variants together; otherwise don't worry.

[yy237]

Thanks!! I checked and they all have different alleles so I think I will keep them as is.