PED file PLINK

Question

[fatma.mokhtar]

Hello,

I want to start with the quality control of my data, but some files are not complete I think;

I have received this PED file (please see attached) https://ibb.co/029NR33 but I do not see all information that should be in:

FID, IID, PID, MID,SEX,PHENO

How can I change that?

Do you think that this form is a PED file? Or did they give it a wrong name?

Best regards,

Fatma Mokhtar

Answer 1

[zx8754]

It is Irregularly-formatted PLINK text files, using below flags that ped file should work fine:

plink --file myFile --no-fid --no-parents --no-sex --no-pheno --make-bed --out myFileBinary

[fatma.mokhtar]

Thank you for your reply. I got an error:

iMac-Fatma-Mokhtar:ArrayData fatma.mokhtar$ ./plink --Go_Cam --no-fid --no-parents --no-sex --no-pheno --make-bed --out myFileBinary
PLINK v1.90b6.18 64-bit (16 Jun 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to myFileBinary.log.
Options in effect:
  --Go_Cam
  --make-bed
  --no-fid
  --no-parents
  --no-pheno
  --no-sex
  --out myFileBinary

Error: Unrecognized flag ('--Go_Cam').
For more information, try "plink --help <flag name>" or "plink --help | more".

[fatma.mokhtar]

I see my mistake now, it was with the file name.

With the command, I have created 3 files: bed, bim, and fam files

Thank you

[fatma.mokhtar]

I have another question, the created FAM file looks like this; ![https://ibb.co/zn2Bg5x][1] Can I now change the gender to male:1 and femal:2? Because I know the gender of the participants? But in the file I know that position or column 5 there we have gender, where we have (0) now, not?

I use ATOM application to open the files? is it ok to change the gender using this application?

Thank you in advance, Fatma Mokhtar