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A typical MaCH command line to estimate phased haplotypes might look like this:
mach1 -d sample.dat -p sample.ped --rounds 20 --states 200 --phase --interim 5 --compact
This will request that MaCH estimate haplotypes for your sample, using 20 iterations of its Markov sampler and conditioning each update on up to 200 haplotypes. A summary description of these parameters follows (but for a more complete description, you should go to the MaCH website):
| <code>--interim 5</code>
| Request that intermediate results should be saved to disk periodically. These will facilitate analyses in case a run doesn't complete.