Anyone knows how to convert Impute2 dosage file to standard Plink files?
I heard that the gtool can help doing that. http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html
Yes, this command is generating a ped file
gtool -G --g example/example.gen --s example/example.sample
You can also specify --ped,--map,--phenotype,--sex and --threshold. Fo example adding --threshold 0.9 will convert the largest genotype probability over the threshold to a ped file genotype.