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Question

Question Posted 09/12/22:
Hello! I've got the WGS SNP data (i.e. GWAS type data) and I've been trying to match it to my phenotype information. I used the PTID from the roster file to make my IID and used the rid as FID, as this seemed to match the .fam file format.
When I tried to merge the phenotype file with my cleaned PLINK dataset none of the phenotypes matched. On closer inspection the IIDs and FIDs don't match. For example the IID for FID 2 in my phenotype file (i.e. rid 2 in my dataset) matches the IID for FID 45 in my genetic dataset.

Have I done the wrong thing in using rid as the basis for FID? If not all advice would be gratefully received.

Thanks ever so much
Lindsey

Response posted 09/18/22 by Kwangsik Nho:

In Plink, the subject IDs were used as xxx_S_xxxx.

Response posted 09/20/22 by Lindsey Sinclair:

Thanks. So just to clarify, what variable should be used as the FID in the PLINK files, or is it missing? I'm struggling to get the phenotypes to merge in with just an IID (i.e. the subject ID).

Response posted 09/22/22 by Kwangsik Nho:

Please use the second column in the plink fam file.

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