Plink Missing Parental Id

Question

[Biomed]

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

[Tg]

This maybe a little bit late but can't you just use option --no-parents?

Answer 1

[Biomed]

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.

[Sudeep]

Just one note : If you use plink --maf command to calculate minor allele frequency the program will use only those samples with missing parental ids, you may have to use --nonfounders option.

Answer 2

[Pierre Lindenbaum]

did you try to use '0' for the parental IDs ?