Ped file looks weird
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10 weeks ago
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When I use less to examine the ped file, it looks like this. Is this normal? Or what might be wrong? The other map, fam, and bim look normal.

enter image description here

ped gwas plink • 276 views
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Is there a reason why you are using ped format? it's incredibly outdated and inefficient (although I know there are some equally old and outdated programs which probably require it).

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10 weeks ago

Check the expected file format here:

https://www.cog-genomics.org/plink/1.9/formats#ped

Contains no header line, and one line per sample with 2V+6 fields where V is the number of variants.

The first six fields are the same as those in a .fam file. The seventh and eighth fields are allele calls for the first variant in the .map file ('0' = no call); the 9th and 10th are allele calls for the second variant; and so on

That being said I thought PED files are formatted more regularly like so:

U_G741-08       U_G741-08       0       0       2       -9      G G     G G     T T     C C    

but technically it does not have to obey that formatting to be valud.

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