Question: Half missing genotype in *.ped files
gravatar for 123sanjanagupta
18 months ago by
123sanjanagupta10 wrote:


I am trying to analyse some genotyping data in PLINK. I started with the raw cluster *.idat files and converted them to PLINK workable files using GenomeStudio. However when I am now trying to use the *.ped and *.map files, I keep getting the following error:

"Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.
Rescanning .ped file... 1%
Error: Half-missing call in .ped file at variant 2, line 2."

This is a copy of the first 5 lines of my ped file:

1   MN_MN-SHE-017   0   0   0   0   G   G   C   C   I   I   G   G   G   G   C   C   C   C   C   C   C   C   G
2   MN_NEW 007 22012014 P   0   0   0   0   G   G   C   C   I   I   G   G   G   G   C   C   C   C   C   C   C   G
3   MN_NEW 021 23042015P    0   0   0   0   G   G   C   C   I   I   G   G   G   G   C   C   C   C   C   C   C   G
4   MN_NOT 009 27082013PM P 0   0   0   0   G   G   C   C   I   I   G   G   G   G   C   C   C   C   C   C   C   G
5   MN_NOT 023 02102013 P   0   0   0   0   G   G   C   C   I   I   G   G   G   G   C   C   C   C   C   C   C   G

Is there anything I can do to fix or overcome this? This is happening across multiple files that I have created this way.

Any help is much appreciated as I have been working on this for over a month now.

Thank you

ADD COMMENTlink modified 18 months ago • written 18 months ago by 123sanjanagupta10

5 rows from ped file do not line up, some rows are missing, and the delimiter, is it space or tab?

ADD REPLYlink written 18 months ago by zx87549.4k

This is what GenomeStudio has produced for me with the PLINK plugin. There are no rows above this. The delimiter is tab and unfortunately there are spaces within the sample ID name as well.

Is there any way that I can overcome this? Or any alternative suggestions how I can get from the raw cluster files to plink workable files? I have over 20 plates and need to combine them altogether.

Thank you very much

ADD REPLYlink written 18 months ago by 123sanjanagupta10

It seems to me your SNP identifiers are not consistent creating the problem. Likely some thing happened with Line 2, 3, 4, 5 to have space in the string, I guess. Replace the space with underscore (_) or, simply remove the spaces to have another try.

ADD REPLYlink modified 15 months ago • written 15 months ago by yifangt8630
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