Question: Plink: Problem With Compound Genotype
0
gravatar for Tyro
7.1 years ago by
Tyro0
Tyro0 wrote:

I am trying to input a file using the compound-genotypes option (as well as several other options), but I get the following error message from PLINK:

ERROR: Problem with compound genotype [ ] should be two characters long

My command line is:

plink --1 --no-fid --no-parents --no-sex --compound-genotypes --map3 --file test

The PED file is:

1 1 gg gg gg gg AA AA AA AA AA gg 
2 0 AA gg gg AA gg gg gg AA AA AA 
3 0 AA AA AA gg AA gg AA gg gg AA 
4 1 gg AA gg AA gg gg gg gg AA AA 
5 1 gg AA gg AA AA AA gg gg AA AA 
6 1 gg gg AA gg AA gg gg AA gg AA 
7 1 gg gg gg gg AA gg gg AA AA AA 
8 0 AA gg AA gg AA gg gg AA AA gg 
9 0 AA AA gg gg gg AA gg gg gg gg 
10 1 gg AA gg AA AA AA gg AA AA gg

The MAP file is:

0 X[0] 0
0 X[1] 0
0 X[2] 0
0 X[3] 0
0 X[4] 0
0 X[5] 0
0 X[6] 0
0 X[7] 0
0 X[8] 0
0 X[9] 0

I am running v1.07 on a Windows XP platform.

Does anyone know what I'm doing wrong? This is just a toy example; I need to convert many large data files to PED/MAP and I'm totally stuck now.

Thanks!

plink • 2.8k views
ADD COMMENTlink written 7.1 years ago by Tyro0

I've narrowed it down to just the --compound-genotypes option. If I remove that option, and add spaces between the alleles, it parses fine. Orthogonally, if I add the missing columns and get rid of the corresponding options, the --compound-genotypes still does not work.

ADD REPLYlink written 7.1 years ago by Tyro0

Oops. In my last comment I should have made it clear that I still need help understanding why the --compound-genotypes option doesn't work.

ADD REPLYlink written 7.1 years ago by Tyro0

Is your map file formatted correctly? I have never seen a plink map without positional data.

ADD REPLYlink written 7.0 years ago by Zev.Kronenberg11k
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