Changes

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:

:<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>

:<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>

= Getting Started =

= Getting Started =

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.  

== Estimating Haplotypes for Your Sample ==

== Estimating Haplotypes for Your Sample ==

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.  

=== Preparing Your Data ===

=== Preparing Your Data ===