Ped file looks weird

Question

[BQ]

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.

[4galaxy77]

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 it's incredibly outdated and inefficient (although I know there are some equally old and outdated programs which probably require it).

Answer 1

[Istvan Albert]

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.