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, 03:38, 28 January 2015
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| == Getting Started == | | == Getting Started == |
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− | Download [http://www.sph.umich.edu/csg/abecasis/MaCH/download/ MaCH] and [http://genome.sph.umich.edu/wiki/Minimac#Download Minimac] or [http://genome.sph.umich.edu/wiki/Minimac2#Download Minimac2]. Furthermore, example data used in this tutorial can be found [http://www.sph.umich.edu/csg/cfuchsb/minimac2_example.tgz here] | + | Download [http://csg.sph.umich.edu/abecasis/MaCH/download/ MaCH] and [http://genome.sph.umich.edu/wiki/Minimac#Download Minimac] or [http://genome.sph.umich.edu/wiki/Minimac2#Download Minimac2]. Furthermore, example data used in this tutorial can be found [http://csg.sph.umich.edu/cfuchsb/minimac2_example.tgz here] |
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| == Minimac and Minimac2 Imputation == | | == Minimac and Minimac2 Imputation == |
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| ./mach1 -d sample.dat -p sample.ped --rounds 20 --states 50 --phase --interim 5 --sample 5 --prefix sample.pp | tee mach.log | | ./mach1 -d sample.dat -p sample.ped --rounds 20 --states 50 --phase --interim 5 --sample 5 --prefix sample.pp | tee mach.log |
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− | This will request that MaCH estimate haplotypes for your sample, using 20 iterations of its Markov sampler and conditioning each update on up to 50 haplotypes. A summary description of these parameters follows (but for a more complete description, you should go to the [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH website]): | + | This will request that MaCH estimate haplotypes for your sample, using 20 iterations of its Markov sampler and conditioning each update on up to 50 haplotypes. A summary description of these parameters follows (but for a more complete description, you should go to the [http://csg.sph.umich.edu/abecasis/MaCH/ MaCH website]): |
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| {| class="wikitable" border="1" cellpadding="2" | | {| class="wikitable" border="1" cellpadding="2" |
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| |style=white-space:nowrap|<code>-d sample.dat</code> | | |style=white-space:nowrap|<code>-d sample.dat</code> |
− | | Data file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin format]. Markers should be listed according to their order along the chromosome. | + | | Data file in [http://csg.sph.umich.edu/abecasis/Merlin/tour/input_files.html Merlin format]. Markers should be listed according to their order along the chromosome. |
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| | <code>-p sample.ped</code> | | | <code>-p sample.ped</code> |
− | | Pedigree file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin format]. Alleles should be labeled on the forward strand. | + | | Pedigree file in [http://csg.sph.umich.edu/abecasis/Merlin/tour/input_files.html Merlin format]. Alleles should be labeled on the forward strand. |
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| | <code>--states 200</code> | | | <code>--states 200</code> |