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, 17:46, 10 March 2011
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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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− | 500 states 10 rounds = 75 min * 10 = 750 min
| + | So, in this case running haplotyping with 500 states and 10 rounds would require 75 min * 10 = 750 min. |
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| + | 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. |
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| == Imputation == | | == Imputation == |