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-genoty 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?
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