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==== Parameters ====
==== Parameters ====
{| class="wikitable" border="1" cellpadding="2"
|- bgcolor="lightgray"
! Parameter
! Description
|-
| <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>
| Iterations of the Markov sampler to use for haplotyping. Typically, using 20 - 100 rounds should give good results. To obtain better results, it is usually better to increase the <code>--states</code> parameter.
|-
| <code>--interim 5</code>
| Request that intermediate results should be saved to disk periodically.
|-
| <code>--phase</code>
| Tell [[MaCH]] to estimate phased haplotypes for each individual.
|-
| <code>--compact</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.
|}
=== Step 2: Imputation ===
=== Step 2: Imputation ===
