Changes

== Minimac Imputation ==

== Minimac Imputation ==

[[Minimac]] relies on a two step approach. First, the samples that are to be analyzed must be phased into a series of estimated haplotypes. Second, imputation is carried out directly into these phased haplotypes. As newer reference panels become available, only the second step must be repeated.

[[Minimac]] and [[Minimac2]] relies on a two step approach. First, the samples that are to be analyzed must be phased into a series of estimated haplotypes. Second, imputation is carried out directly into these phased haplotypes. As newer reference panels become available, only the second step must be repeated.

=== Pre-phasing - MaCH ===

=== Pre-phasing - MaCH ===

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=== Imputation into Phased Haplotypes - minimac ===

=== Imputation into Phased Haplotypes - minimac(2)===

Imputing genotypes using '''minimac''' is a straightforward process: after selecting a set of reference haplotypes, plugging-in the target haplotypes from the previous step and setting the number of rounds to use for estimating model parameters (which describe the length and conservation of haplotype stretches shared between the reference panel and your study samples), imputation should proceed rapidly. Because marker names can change between dbSNP versions, it is usually a good idea to include ''aliases'' file that provides mappings between earlier marker names and the current preferred name for each polymorphism.

Imputing genotypes using '''minimac(2)''' is a straightforward process: after selecting a set of reference haplotypes, plugging-in the target haplotypes from the previous step and setting the number of rounds to use for estimating model parameters (which describe the length and conservation of haplotype stretches shared between the reference panel and your study samples), imputation should proceed rapidly. Because marker names can change between dbSNP versions, it is usually a good idea to include ''aliases'' file that provides mappings between earlier marker names and the current preferred name for each polymorphism.

The minimac command line would look like this:

The minimac command line would look like this:

  ./minimac --refHaps hapmap.hap --refSnps hapmap.snps --haps sample.pp.gz --snps sample.snps --prefix sample.imp | tee minimac.log

  ./minimac --refHaps hapmap.hap --refSnps hapmap.snps --haps sample.pp.gz --snps sample.snps --prefix sample.imp | tee minimac.log

A detailed description of all minimac options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters:

 

 

 

A detailed description of all minimac(2) options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters:

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You can speed-up things by running minimac in parallel by launching the [http://genome.sph.umich.edu/wiki/Minimac#Multiprocessor_Version minimac-omp] version. On our cluster 4 cpus per minimac is optimal (--cpus 4).

You can speed-up things by running minimac in parallel by launching the [http://genome.sph.umich.edu/wiki/Minimac2#Multiprocessor_Version minimac2-omp] version. On our cluster 4 cpus per minimac(2) is optimal (--cpus 4).

  ./minimac-omp --cpus 4 --refHaps hapmap.hap --refSnps hapmap.snps --haps sample.pp.gz --snps sample.snps --prefix sample.imp | tee minimac-omp.log

  ./minimac-omp --cpus 4 --refHaps hapmap.hap --refSnps hapmap.snps --haps sample.pp.gz --snps sample.snps --prefix sample.imp | tee minimac-omp.log

== Imputation quality evaluation ==

== Imputation quality evaluation ==