Impute2 dosage file into standard Plink files

Question

[rahapazoki]

Hi all,

Anyone knows how to convert Impute2 dosage file to standard Plink files?

Thanks

Answer 1

[Jimbou]

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. For example adding --threshold 0.9 will convert the largest genotype probability over the threshold to a ped file genotype.

Answer 2

[rahapazoki]

I heard that the gtool can help doing that. http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html