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399 bytes added, 03:32, 12 October 2010
==== Parameters ====
-p sample.ped
pedigree file in [ Merlin] format
{| class="wikitable" border="1" cellpadding="2"|- bgcolor="lightgray"! Parameter ! Description|- | <code>-d sample.dat</code>dat | Data file in [ Merlinformat] format. It is important that markers should be listed according to their order along the chromosome.|- | <code>--rounds Rp sample.ped</code>how many iterations of the Markov sampler | Pedigree file in [ Merlin format]. It is important that alleles should be runlabeled on the forward strand.|- | <code>--states ST200</code>use a random subset | Number of ST haplotypes as reference. We recommend values between 200 - 500to consider during each update. More states result in more accurate Increasing this value will typically lead to better haplotypes, but are computational more expensive can also dramatically increase computing time and require more memoryrequirements. A value of 100 - 400 is typical.|- | <code>--interim Irounds 50</code>output a set | Iterations of bestthe Markov sampler to use for haplotyping. Typically, using 20 -guess haplotypes every I 100 rounds by building consensus from all previous Markov iterationsshould give good results. These intermediate haplotypes can be used for imputationTo obtain better results, it is usually better to increase the <code>--states</code> parameter.|- | <code>--sample SAinterim 5</code>output a set of haplotypes every SA rounds based on random sampling from the last Markov iteration. These | Request that intermediate results can should be combined and used as input for the imputation processsaved to disk periodically.|- | <code>--phase </code> enables | Tell [[MaCH]] phasing modeto estimate phased haplotypes for each individual.|- | <code>--compact</code>reduces | Tell [[MaCH]] to reduce memory use at the amount cost of memory needed dramatically, but doubles execution timeapproximately doubling runtime. This option is recommended for most GWAS scale datasets and computing platforms.|}
=== Step 2: Imputation ===

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