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Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and 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 uses M3VCF 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 M3VCF files. M3VCF 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.
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