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= Introduction =

= Introduction =

'''Minimac3 ''' is a lower memory and more computationally efficient implementation of [http://genome.sph.umich.edu/wiki/Minimac2 minimac2]. It is an algorithm for genotypic imputation that works on phased genotypes (say from [http://genome.sph.umich.edu/wiki/MaCH MaCH]). minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. This algorithm analyzes only the unique sets of haplotypes in small genomic segments, thereby saving on time-complexity, computational memory but no loss in degree of accuracy.

'''Minimac3 ''' is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in [Minimac] and [Minimac2|minimac2]. minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. It accomplishes this by identifying repeat haplotype patterns and using these to simplify the underlying calculations, with no loss of accuracy.

Minimac3, apart from performing imputation, also creates [[M3VCF Files|<font face=Courier>M3VCF</font> files]] (customized minimac3 VCF files) which are able to store reference panel information in a compact form, thus saving on memory and time required to read large datasets. User will have an option to use the binary code to either just convert VCF files to <font face=Courier>M3VCF</font> files or to perform imputation as well. The code can also take a previously generated <font face=Courier>M3VCF</font> file as input for the reference panel. <font face=Courier>M3VCF</font> files can also store pre-calculated estimates of recombination fraction and error, which can be used for later runs of imputation.  The latest version of Minimac3 also allows output in the form of VCF files for easier data manipulation in downstream analysis.

Minimac3 uses [[M3VCF Files|<font face=Courier>M3VCF</font> files]] (customized minimac3 VCF files) to store reference panel information in a compact form, thus saving on memory and time required to read large datasets. Users can use Minimac3 to convert standard VCF files to <font face=Courier>M3VCF</font> files. <font face=Courier>M3VCF</font> files can also store pre-calculated estimates of recombination fraction and error, which speeds up later rounds of imputation.  Minimac3 outputs results in the form of standard VCF files for easy data manipulation in downstream analysis.

= Download =

= Download =

'''Minimac3 ''' is available as an undocumented release version. The source files are available for download here and commonly used reference panels in <code>M3VCF</code> format are available for download in [[Minimac3 Imputation Cookbook#Reference Panels for Download | Reference Panels]]. The authors would really appreciate if users would use it on their data set and let us know of possible bugs to be fixed.  

'''Minimac3 ''' is currently available as a pre-release release version. Commonly used reference panels in <code>M3VCF</code> format are available for download in [[Minimac3 Imputation Cookbook#Reference Panels for Download | Reference Panels]]. The authors would really appreciate if users report possible bugs by e-mailing [[mailto:sayantan@umich.edu|Sayantan Das]].

 

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   /bin/Minimac3 --help

   /bin/Minimac3 --help

= Contact =

= Contact =

In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].

In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].