I am working on GWAS and planning to use chromopainter, finestructure and globetrotter from plink. I am trying to convert plink 1/2 file format to chromopainter file by using the plink2chromopainter.pl script as it is advised in the website. Here what I did : ./plink2chromopainter.pl -p=myped.ped -m=mymap.map -o=mydataphase.phase -donor=mydonor.donor -rec=myrec.rec
Here is the error: SNPs must be output in 0/1 format, but we received 0 (-1)= -1. Do you need to run with/without -a?
What does exactly this error mean? Which plink format is really need by the script to work fine?
Where was my mistake?
Thank you very much for your answers.
Do you have missing data in your plink file (i.e. 0s)? If so, that could be the problem. Chromopainter does not allow for missing data - you should either remove those positions or impute them.
Hi Saioa,
Yes, there might some missing data due to merge process as the genotype rate decreased.
I am looking for a better way to keep that genotype rate as high as possible during the merging. I already ask advice to Christopher Chang, the plink expert.
And will advance to chromopainter, finestructure and globetrotter.
Thank you for the answer
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