Difference Between .Pre And .Ped File (Problems With Snpspd

Question

[ludiklobucar]

Hi,

I am trying to input files into SNPSpD which requires .pre and .map files. I hoped that, as .pre and .ped files are quite similar (as far as I know), I can just phenotype column and change file extension, but it doesn't work. I couldn't find a program that would convert file from .ped to .pre, only other way around. Does somebody have a suggestion what I could do? My .ped and .map files are in standard format for PLINK. Thank you very much.

Zeljka

Answer 1

[Matt Shirley]

Could you give a short example of what the first few columns and rows of your ped file look like? If I understand this correctly, you have tried removing the phenotype column (column number 6) from your *.ped file and renamed the resulting file *.pre. If so, then there must be something wrong with your per file, as the pre file columns are:

 Family ID
 Individual ID
 Paternal ID
 Maternal ID
 Sex (1=male; 2=female)

And ped file columns are:

 Family ID
 Individual ID
 Paternal ID
 Maternal ID
 Sex (1=male; 2=female)
 Phenotype

You might try cut -f1-5,7- file.ped > file.pre, or visit Galaxy and try the cut column tool.

Answer 2

[ludiklobucar]

Yes, you understood correctly what I tried to do. It turned out that the .ped/.pre files were not the problem, but the .map file. I assumed that the .map file was in standard format, first column for chromosome number, but it was not. Program expects first column to be markerid. Thank you very much, and sorry for taking your time :(, I should have been more careful.

Bye, Zeljka

Answer 3

[Varun]

Hi Zeljka,

I am having the same problem, but unfortunately am not able to sort it out yet. Can you tell me what you did to correct the MAP files, please?

Thanks!