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== Pre-phasing ==
== Pre-phasing ==
For the pre-phasing step the cost for increasing the number of states is quadratically and the cost for additional rounds is linear.
For the pre-phasing step, cost increases quadratically with the number of states and linearly with the number of rounds. The following table provides a simple example.
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So, in this case running haplotyping with 500 states and 10 rounds would require 75 min * 10 = 750 min.
Typically, haplotype quality improves rapidly with the number of states but only slowly with the number of rounds. We recommend running ~20 rounds of the MaCH haplotyper and selecting a number of states as high as your patience will allow.
== Imputation ==
== Imputation ==
