Minimac3

Useful Wiki Pages

There are a few pages in this Wiki that may be useful to for Minimac3 users. Here are links to a few:

• Minimac3 Overview Page

• Minimac3 Usage and Documentation

• Minimac3 Imputation Cookbook (Recommended for New Users!!)

• Minimac3 Examples

• M3VCF Files

Introduction

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 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.

Download

Minimac3 is currently available as a pre-release release version. Commonly used reference panels in M3VCF format are available for download in Reference Panels. The authors would really appreciate if users report possible bugs by e-mailing [Das].

Description	Download Link
Minimac3 Executable	UNIX Users
Minimac3-omp Executable (for parallel computing)	UNIX Users
Minimac3 Source Files	UNIX Users

Usage

Users should follow the following steps to compile Minimac3 (if they downloaded the source files) or should skip them (if they downloaded the binary executable).

## EXTRACT MINIMAC3 AND COMPILE
 
tar -xzvf Minimac3.v1.0.0.tar.gz
cd Minimac3/
make

A typical Minimac3 command line for imputation is as follows

../bin/Minimac3 --refHaps refPanel.vcf \ 
                --haps targetStudy.vcf \
                --prefix testRun

Here refPanel.vcf is the reference panel used in VCF format (e.g. 1000 Genomes), targetStudy.vcf is the phased GWAS data in VCF format, and testRun is the prefix for the output files. Some commonly used reference panels are available for download in Reference Panels. See wiki page on Detailed Usage and Imputation Cookbook for further details on using Minimac3 for imputation analysis.

Users can always type the following for further support:

 /bin/Minimac3 --help

Contact

In case of any queries and bugs please contact Sayantan Das.