Pedigree information

Question

[heureuse]

Hello,

I have bed, bim, fam files. I used the tool KING to infer relations and find parents offspring. now I have parents and children informations but I don't know between the parents who is the mother and who is the father.

I need help please.

Thanks

[dthorbur]

You haven't asked a question, so we don't really know what you are after. I suspect you want to identify which of them is the mother and the father. If you have whole genome data, and the species you are using has sex chromosomes, you could look for reads mapping to the Y (or analogous) chromosome.

[heureuse]

That was the question. Thank you for the answer. It helps.

[bk11]

Since you have plink (bed/bim/fam) files, sex information is stored in the 5th column of the .fam file. If that information is missing and if you also have data in sex chromosomes, you can easily impute sex using following command in plink:

plink --bfile data --impute-sex --make-bed --out newfile

Your newfile.fam will have sex info in 5th column ('1'=male, '2'=female and '0'=unknown).