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, 03:53, 11 September 2014
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− | A good rule of thumb is that minimac should take about 1 hour to impute 1,000,000 markers in 1,000 individuals using a reference panel with 100 haplotypes. Performance should scale linearly with respect to all these factors. So, your approximate computing time in hours should be about: | + | A good rule of thumb is that minimac2 should take about 1 hour to impute 1,000,000 markers in 1,000 individuals using a reference panel with 1000 haplotypes. Performance should scale linearly with respect to all these factors. So, your approximate computing time in hours should be about: |
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| :<math> | | :<math> |
− | E(\mbox{Run Time in Hours}) = N_{markers} * N_{individuals} * N_{haplotypes} * 10^{-11} | + | E(\mbox{Run Time in Hours}) = N_{markers} * N_{individuals} * N_{haplotypes} * 10^{-10} |
| </math> | | </math> |
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| :<math> | | :<math> |
− | E(\mbox{Run Time in Hours}) = N_{markers} * ({N_{individuals} + N_{rounds} * N_{states} * 0.75 }) * N_{haplotypes} * 10^{-11} | + | E(\mbox{Run Time in Hours}) = N_{markers} * ({N_{individuals} + N_{rounds} * N_{states} * 0.75 }) * N_{haplotypes} * 10^{-10} |
| </math> | | </math> |
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| = Getting Started = | | = Getting Started = |
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− | Using minimac for genotype imputation involves two steps. First, you will have to estimate haplotypes for your entire sample -- this will be the more computationally demanding step. Once that is done, you will be ready to quickly impute missing genotypes using the reference panel of your choice. | + | Using minimac2 for genotype imputation involves two steps. First, you will have to estimate haplotypes for your entire sample -- this will be the more computationally demanding step. Once that is done, you will be ready to quickly impute missing genotypes using the reference panel of your choice. |
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| == Estimating Haplotypes for Your Sample == | | == Estimating Haplotypes for Your Sample == |
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− | For the haplotyping step, we current recommend using [[MaCH]] with the --phase command line option. As input [[MaCH]] will need [[Merlin]] format pedigree and data files. All markers should be ordered according to their physical position and alleles should be labeled on the forward strand. | + | For the haplotyping step, you can use [[MaCH]] with the --phase command line option. As input [[MaCH]] will need [[Merlin]] format pedigree and data files. All markers should be ordered according to their physical position and alleles should be labeled on the forward strand. |
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| === Preparing Your Data === | | === Preparing Your Data === |