PLINK .ped file issue

Question

[plinknoob23]

Hi everyone,

relative newbie here (non-bioinformatics background; got to know EWAS and TWAS before, but have no experience with plink).

I am trying to run a GWAS using a .ped and a .map file (got nothing else apart from the raw .idat files). I am trying to use plink for convert the obsolete .ped/.map files into something more usable. I keep getting error messages when trying to convert into bed/bim/fam format, though.

Precisely, when I run:

plink --file FILENAME --make-bed --out FILENAME_out --id-delim " "

I get the error message

Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.
Rescanning .ped file... 0%
Error: Half-missing call in .ped file at variant 1, line 1.

I have been able to resolve the problem and obtain bed/bim/fam files when I used a small (10-phenotype) subset of my data in Excel and deleted the first line (i.e., eliminating variant 1, line 1), which just contained "V1" in the first cell (equating to "variant 1, line 1", I guess).

Now I would like to either specify that plink should ignore the first line, or to delete the first line in the entire file (which is not possible in Excel because the file is too large).

I am sorry if it should be obvious how to do this, but I feel a bit overwhelmed with the extensive plink documentation and have tried some options from there without success. I would very much appreciate your help!

[bk11]

If deleting the first line of .ped file works for you then you can do sed '1d' old.ped > new.ped. It will delete first line of your ped file. You may have to delete the line in map file in the same way. Make sure the newly generated .ped and .map files have the same prefix before running- plink --file new --make-bed --out new