From Genome Analysis Wiki
Revision as of 21:19, 18 December 2016 by Santy.8128 (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search
  • Introducing DosageConvertor, a tool to convert imputed data in VCF format to other formats, such as MaCH or PLINK.
  • Please join our NEW mailing list to get updates about future releases, bug fixes or post queries.
  • Download New Version 2.0.1 !!! (Updated June 2016) !!! See ChangeLog for details !!!

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 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.


Minimac3 is currently available as a release version. Commonly used reference panels in M3VCF format are available for download in Reference Panels.

Please join our NEW mailing list to get updates about future releases or report possible bugs or email them to Sayantan Das.

VERSION: 2.0.1 !!! (Updated 6.6.2016) !!!

Github Repo: Users can clone from github repository as well : Minimac3 Github

Cloning from GitHub is recommened so that updates can be easily pulled back !!!

Description Download Link
Source Files UNIX Users
Binary Executable UNIX Users

Binary executables are NOT guaranteed to run on every LINUX machine. Please compile from source files if you have trouble with the executable, or else contact the author Sayantan Das..


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).

tar -xzvf Minimac3.v2.0.1.tar.gz
cd Minimac3/

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

Reference Panels for Download

Some commonly used reference panels are available for download here:

Chr X Haplotypes for 1000 Genomes Phase 3 have been updated on Oct 20 to include multi-allelic variants as well (split as bi-allelic variants) !!!

Reference Panel Number
of Samples
File Format Parameter
Chromosomes Link
1000 Genomes

Phase 3
(version 5)

2,504 VCF - 1-22,X Download
M3VCF YES 1-22,X Download
NO 1-22,X Download
VCF,M3VCF YES X Download
1000 Genomes

Phase 1
(version 3)

1,092 VCF - 1-22,X Download
M3VCF YES 1-22,X Download
NO 1-22,X Download
VCF,M3VCF YES X Download


If you use minimac3 please cite:

Das S, Forer L, Schönherr S, Sidore C, Locke AE et al. Next-generation genotype imputation service and methods. Nature Genetics 2016; 48, 1284–1287 (2016) doi:10.1038/ng.3656[1]


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