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, 03:19, 12 October 2010
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| ==== Parameters ==== | | ==== Parameters ==== |
− | --refHaps ref.hap
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− | Reference haplotypes (e.g. [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page])
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− | --refSnps ref.snps
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− | Reference SNPs (e.g. [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page])
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− | --haps target.hap
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− | Target haplotypes (from the pre-phasing step)
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− | --snps target.snps
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− | Target snps (from the pre-phasing step)
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− | --rounds [5]
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− | how many rounds should be run to optimize the model parameters: (i) error rate for each marker (*.erate) and (ii) crossover rates (*.rec) for each interval.
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− | --states [200]
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− | how many haplotypes to use for parameter optimization.
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− | --em
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− | use an e-m algorithm, instead of mcmc, for parameter optimization
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− | --rec file.rec
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− | use crossover rates from this file
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− | --erate file.erate
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− | use error rates from this file
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− | --prefix [minimac]
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− | prefix for output files, default minimac
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| + | {| class="wikitable" border="1" |
| + | |- |
| + | ! Parameter |
| + | ! Description |
| + | |- |
| + | | <code>--refSnps ref.snps</code> |
| + | | List of SNPs in the reference panel |
| + | |- |
| + | | <code>--refHaps ref.hap</code> |
| + | | Reference haplotypes (e.g. from [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page]) |
| + | |- |
| + | | <code>--snps target.snps</code> |
| + | | SNPs in phased haplotypes. These should largely be a subset of the SNPs in the reference panel. |
| + | |- |
| + | | <code>--haps target.hap</code> |
| + | | Phased haplotypes where missing genotypes will be imputed. |
| + | |- |
| + | | --rounds 5 |
| + | | Rounds of optimization for model parameters, which describe population recombination rates and per SNP error rates. |
| + | |- |
| + | | --states 200 |
| + | | Maximum number of reference (or target) haplotypes to examined during parameter optimization. |
| + | |- |
| + | | --prefix imputed |
| + | | Optionally, a string that is used to help generate output file names. |
| + | |} |
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| == Related Pages == | | == Related Pages == |