Introduction

Minimac3 is a lower memory and more computationally efficient implementation of minimac2. It is an algorithm for genotypic imputation that works on phased genotypes (say from MaCH) and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.

This wiki page is designed to give users a detailed explanation of the info file outputted by Minimac3.

Info File Descriptors

The available options of Minimac3 are explained in detail below. See wiki page on Examples and Full list of Options for more details. There is also a wiki-page on Minimac3 Imputation Cookbook which is recommended for new users !

SNP

The SNP identifier for the variant. This is usually in the form of chr:position, but could be the rsid of the variant if the user had selected --rsid during the Minimac3 run.

REF, ALT

These are the reference and alternate alleles for the variant as imported from the reference panel file (either VCF or M3VCF)

Major, Minor

These are the major and minor alleles for the variant based on the reference allele frequency (and NOT imputed dosage frequency)

DoseMAF

This is the minor allele frequency of the variant in the imputed dosage data (and NOT the reference panel). [NOTE: The DoseMAF does NOT always correspond to the allele frequency of the listed minor allele, since sometimes the imputed minor allele is different from the reference minor allele]

Download

Minimac3 is available as an undocumented release version. The source files (and binary executable) are available for download in Source Files and commonly used reference panels in VCF and M3VCF formats are available for download in Reference Panels.