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'''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 [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, 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, 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.

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