Plink MAF Calculation

Question

[mitchez]

Hallo,

the input format for PLINK ped files requires: FamilyID, IndividualID,Paternal ID, MaternalID,Sex,Pheno...

I figured out that when you set Paternal ID and Maternal ID to 1 instead of 0, PLINK will not calculate a MAF instead produce NAs.

Do you have an explanation why the MAF is not calculated ?

Thanks for your help,

m

Answer 1

[Maxime Lamontagne]

If you put 1 or anything else instead of 0, it means the father and/or the mother of this individual are in the dataset. You are giving PLINK the individual ID of the mother and the father. PLINK will try to find these subjects and I guess you don't have these individuals. Also, if you put 1 in both Paternal and Maternal ID, it means the father and the mother of this individual are the same person. I guess PLINK gives you NAs because of this.