<p>Hi I am trying to put together a plink ped file but I couldn't find how to depict missing maternal and paternal ids. You can give an argument if you have no parent ids in your file but I only miss some. For sex and phenotype you have missing data codes but what about the parental ids?
To put it differently how exactly do you depict the family relationships in the ped file format for plink?
Thanks </p>

<p>I got it. You just give 0 to parents maternal id and paternal id. This simply means that the parents' parents are missing and as long as you supply the true parental ids for the kids PLINK takes care of the rest.</p>