Plink warning: different genetic position for marker xx

Question

[Selenocysteine]

Hi everyone,

I am trying to merge two datasets obtained with two different chips (Illumina HumanOmni2.5-8 v1.2 and HumanOmni2.5-8 v1.1, see http://support.illumina.com/array/array_kits/humanomni2_5-8_beadchip_kit/downloads.html) with plink. However, the software gives me this error (Plink warning: different genetic position for marker xx) for multiple markers. What is the possible reason for this? How am I supposed to fix it?

Thanks!

[Sam]

Are you sure they have the same build? e.g. hg19 vs hg18

Consider their version difference, that might be the case.

[Selenocysteine]

It is possible, but I only got the final plink files, so I am not quite sure about what data they used to generate the .ped and .map file from the raw data.

[Sam]

Then you can use R to read the map files, then do a manual mapping and find out the Snps that has unmatched location. You can then go to dbSnp to check whether if their build is different or if the Snp simply changed (sometimes they update the location).

[Selenocysteine]

Yes I'll probably do it this way thanks :)