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, 03:34, 12 October 2010
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| | <code>-d sample.dat</code> | | | <code>-d sample.dat</code> |
− | | Data file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin format]. It is important that markers should be listed according to their order along the chromosome. | + | | 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. |
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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]. It is important that alleles should be labeled on the forward strand. | + | | 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. |
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| | <code>--states 200</code> | | | <code>--states 200</code> |
− | | Number of haplotypes to consider during each update. Increasing this value will typically lead to better haplotypes, but can also dramatically increase computing time and memory requirements. A value of 100 - 400 is typical. | + | | Number of haplotypes to consider during each update. Increasing this value will typically lead to better haplotypes, but can dramatically increase computing time and memory use. A value of 100 - 400 is typical. |
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| | <code>--rounds 50</code> | | | <code>--rounds 50</code> |
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| | <code>--compact</code> | | | <code>--compact</code> |
− | | Tell [[MaCH]] to reduce memory use at the cost of approximately doubling runtime. This option is recommended for most GWAS scale datasets and computing platforms. | + | | Reduce memory use at the cost of approximately doubling runtime. This option is recommended for most GWAS scale datasets and computing platforms. |
| |} | | |} |
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