merlin .ped file
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Entering edit mode
5.4 years ago
User6891 ▴ 290

Hi,

I'm creating a .ped file for Merlin to do linkage analysis for SNParray data.

I have a family of 12 members, but for some siblings, I only have one parent available, so in the .ped file, the father ID might be '8', but the mother id '0' for unknown. 

When I do this, pedstats is giving me an error: Parent named 0 for Person 5 in Family 1 is missing

Any idea on how to solve this?

 

linkage merlin pedigree • 2.7k views
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5.4 years ago
dhibar ▴ 40

You have to include an entry for each parent in the Ped file even if they are missing. Also, even if a parent is missing you should give them a non-zero ID if the other parent isn't missing. So if the parent (father) is missing from family 1 it currently looks like this:

Family1 Sib1 Father0 Mother8 1

And you need to change it such that the missing father for the group still gets a unique ID:

Family1 Sib1 Father7 Mother8 1

In addition, you need to add the father to your pedigree file:

Family1 Father7 0 0 1

Notice that both parents are missing for Father7 so you can set both to 0 and there isn't the expectation that they will be listed in the Ped file somewhere.

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But my .ped file, used as input for merlin, also contains the marker genotypes (from the SNP-array). But I have no data for Father7, so can I then just add the first 5 columns and leave the rest empty?

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You can provide a "linking file" that lists the full set of subjects like mentioned above with the Ped file that has your genotypes. In merlin you would do this by separating them with a comma:

merlin -p familystructure.ped,pheno.ped -d familystructure.dat,pheno.dat [...]
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I'm sorry but that's not completely clear for me.

So the pheno.ped should be my original file with the individuals for whom I have marker data?

And then the familystructure.ped should be a .ped file with only 5 columns in which there are lines for all individuals even those without marker data?

pheno.dat is then my original .dat file. But what needs to be inside familystructure.dat?

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Problem solved:

pheno.ped = all genotyped individuals (6 columns + marker data)

familystructure.ped = all individuals (6 columns)

familystructure.dat = only one line, with disease condition (A condition)

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