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

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!

snp gene genome
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updated by chrchang523 chrchang523 • written by yy237 • yy237

1 answer

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

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written by chrchang523 chrchang523

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

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written by yy237 • yy237

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