From Genome Analysis Wiki
==== Parameters ====
pedigree file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin] format
-d sample.dat dat file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin] format - -rounds R how many iterations of the Markov sampler should be run. --states ST use a random subset of ST haplotypes as reference. We recommend values between 200 - 500. More states result in more accurate haplotypes, but are computational more expensive and require more memory. -- interim I output a set of best- guess haplotypes every I rounds by building consensus from all previous Markov iterations. These intermediate haplotypes can be used for imputation. -- sample SA output a set of haplotypes every SA rounds based on random sampling from the last Markov iteration. These intermediate results can be combined and used as input for the imputation process. --phase enables [[MaCH]] phasing mode. --compact reduces the amount of memory needed dramatically, but doubles execution time.
=== Step 2: Imputation ===