Question: Plink Missing Parental Id
3
gravatar for Biomed
8.2 years ago by
Biomed4.4k
Bethesda, MD, USA
Biomed4.4k wrote:

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

plink ped • 3.1k views
ADD COMMENTlink modified 8.2 years ago by Tg310 • written 8.2 years ago by Biomed4.4k

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

ADD REPLYlink modified 11 days ago by Ram17k • written 7.7 years ago by Tg310
6
gravatar for Biomed
8.2 years ago by
Biomed4.4k
Bethesda, MD, USA
Biomed4.4k wrote:

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.

ADD COMMENTlink modified 8.2 years ago • written 8.2 years ago by Biomed4.4k

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.

ADD REPLYlink modified 11 days ago by Ram17k • written 7.7 years ago by Sudeep1.6k
4
gravatar for Pierre Lindenbaum
8.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum112k wrote:

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

ADD COMMENTlink written 8.2 years ago by Pierre Lindenbaum112k
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