Recoding plink file from 12 to 01

Question

[dirranrak]

Hi all,

I tried to use Plink2chromopainter.pl to convert plink file to chromopainter file. I have plink file recoded 12 but I need to recode the file to 01 before using the program. I did use --recode 01 --output-missing-genotype 3. I have red the plink manual but I still got a strange content in the file with very few variants. What should be the problem? What should I do?

More details:

I am trying to use finestructure, I need chromopainter file to be able to work with. I have plink ped file recoded 12, I need to convert the plink file into chromopainter format by using plink2chromopainter.pl. I followed the instruction from the finestructure website. I ran the conversion script as told but I get an error:

SNPs must be in 0/1 format, but we received 0 (-1) = -1. Do you need to run with/without -a?

Thank you very much

[Ram]

I think OP is talking about a tool found here: https://people.maths.bris.ac.uk/~madjl/finestructure/manualse11.html

OP, please always provide context.

[Ram]

need to recode the file to 01 before using the program

• which program?
• where does it say you need to recode the file to 01?
• why does a tool want you recoding back and forth for its own internal compatibility? That's a badly designed tool.

[dirranrak]

Hi, sorry for not giving enough details. I am trying to use finestructure, I need chromopainter file to be able to work with. I have plink ped file recoded 12, I need to convert the plink file into chromopainter format by using plink2chromopainter.pl. I followed the instruction from the finestructure website. I ran the conversion script as told but I get an error: SNPs must be in 0/1 format, but we received 0 (-1) = -1. Do you need to run with/without -a?

Thank you for your answer

[Ram]

Do not add an answer unless you're answering your original question. What you're doing here is adding more information, which you should do by editing your original post.

I'll do what's needed for you now, but please be more careful in the future.

[Ram]

The tool mentions you need the input file in 12 format but errors out saying it needs them in 01 format? You mention you recoded in 01 format, and then you say you recoded in 12 format, which is it? Please edit you question and add the exact command you used. Also, try your command with a -a only if your data is 01 recoded.