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0
Entering edit mode
2.1 years ago
bsmith030465 ▴ 200

Hi,

I was trying to convert my ped file to a bed file with the command

plink --file mysamples --make-bed


However, I get the error:

 Scanning .ped file...
Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.

Error: Half-missing call in .ped file at variant 1, line 1.


The first line of my ped file (testing with only 15 variants) is:

FES2356 ES1249 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 1 1 0 1 0 1 0


Where am I going wrong?

thanks!

EDIT:

PLINK v1.90b4.6 64-bit (15 Aug 2017) www.cog-genomics.org/plink/1.9/ (C) 2005-2017 Shaun Purcell, Christopher Chang GNU General Public License v3

1. Error: Half-missing call in .ped file at variant 1, line 1.
0
Entering edit mode
2.1 years ago

‘0’ is normally the missing-genotype code. The body of a .ped line is supposed to look like “A C A A T G ...”.