Detritus Wiki

http://mathgen.stats.ox.ac.uk/impute/impute_v2.html

• -g <input file> - database to input (see format below)
• -m <map> - recombination map as 1000Genome or something like this
• -int <lower> <upper> - interval to make the imputation

http://www.stats.ox.ac.uk/~marchini/software/gwas/file_format.html

First convert the binary files to .ped and .map if needed

http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml

then you can use gtool,

http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html

in particular, http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html#PED to GEN Conversion

gtool -P --ped example/example.ped --map example/example.map --og example/out.gen --os example/out.sample

Before this some awkward work need to be done

Look an example here