Using Plink To Convert Files

Question

[Tim]

Hey,

I am trying to use PLINK to convert .ped and .map output into another format. As many know Affymetrix SNP chips used to be coded in AA, AB, BB manner and this format has often been recoded into 1,0,-1. I would need to convert my ACTG .ped file into a 1,0,-1 file and I was wondering whether there is a way in PLINK to do that - could somebody help me out?

Tim

Answer 1

[zx8754]

How about use plink --recode12 option, and then use sed to convert 1,2 plink ped file to 1, 0, -1

plink --file data --recode12 --tab --out file12

Assuming "1 1"=1, "1 2"=0, "2 2"=-1:

sed 's/1 1/1/g' file12.ped | sed 's/1 2/0/g' | sed 's/2 2/-1/g' > file101.ped

Answer 2

[Tim]

Hey

thanks for the response - just to make sure did you guess that 1 1=1 and 1 2=0 and 2 2=-1 or is this convention? Moreover, is the 'sed' line ready to be intered into plink? Doesn't it have to start with plink --file.....like your first line ?

[Hernán]

sed is another program separate from plink and it should be entered apart. If you are using Windows, you may install MinGW or Cygwing which includes a shell where you can find sed. Check for unix2dos if your files were generated under Unix. If you are under a Unix-like OS, sed is already there.

[zx8754]

"1 1=1 and 1 2=0 and 2 2=-1" - is my assumption, it is not a convention. Also, not sure how you would code NoCalls.