| <code>-d sample.dat</code>
| Data file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin format].
It is important that markers should be listed according to their order along the chromosome.
| <code>-p sample.ped</code>
| Pedigree file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin format].
It is important that alleles should be labeled on the forward strand.
| <code>--states 200</code>
| Number of haplotypes to consider during each update. Increasing this value will typically lead to better haplotypes, but can
also dramatically increase computing time and memory requirements. A value of 100 - 400 is typical.
| <code>--rounds 50</code>
Tell [[MaCH]] to reduce memory use at the cost of approximately doubling runtime. This option is recommended for most GWAS scale datasets and computing platforms.