From Genome Analysis Wiki
== Why and how to perform a 2-step imputation? ==
# step 2:
mach1 -d sample.dat -p sample.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip --errorMap par_infer.erate --crossoverMap par_infer.rec --mle --mldetails > mach.imp.log
In step2, each individual is imputed independently and can therefore be split into as many as n (sample size) jobs for each chromosome for parallelism.