Re: convert .ped .map to bfile and FID,IID change the column

[Christopher Chang]

Please post a set of input files and a full .log file that can be used to replicate what you're seeing.

On Sunday, May 16, 2021 at 10:03:16 AM UTC-7 panm...@yeah.net wrote:

When I run plink --file chr1 --make-bed --out chr1, I found my chr1.fam file FID, IID positions are changed compare to the Original file.

Original file:

2 S-01 0 0 2 -9

and my chr1.fam file:

S-01 2 0 0 2 -9

I don't understand why I got the position changed. And how could I knwo if the gen files are corrected.

Best 

Ammy

[潘梦宇]

Thanks for your replying. 

I tried to merge ch1 to ch22 map and ped files, I  work on TSD(Services for sensitive data) where I cannot copy lines. So I PrtSc my log file and my ch1.map file.

ped file has many lines I didn't put them here, these look quite normal, I am not sure how the plink --file --make-bed to identify which is FID and which is IID. But they changed the columns actually. I have solved by calling --update-ids to re-order them. Not sure if I can do in this way?

Best Regards

Ammy