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'''Minimac4 ''' is a latest version in the series of genotype imputation software - preceded by [[Minimac3|Minimac3]] (2015), [[Minimac2|Minimac2]] (2014), [[Minimac|minimac]] (2012) and [[MaCH|MaCH]] (2010). '''Minimac4''' is a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality.
'''Minimac4 ''' is a latest version in the series of genotype imputation software - preceded by [[Minimac3|Minimac3]] (2015), [[Minimac2|Minimac2]] (2014), [[Minimac|minimac]] (2012) and [[MaCH|MaCH]] (2010). '''Minimac4''' is a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality.
The Minimac3 mailing list has been renamed as the Minimac4 mailing list. If you were already a member, no need to re-join. If not, please join our [https://groups.google.com/forum/embed/?place=forum/minimac4-help&umich.edu| mailing list] to get updates about future releases or report possible bugs or email them to [mailto:sayantan@umich.edu Sayantan Das].'''
The Minimac3 mailing list has been renamed as the Minimac4 mailing list. If you were already a member, no need to re-join. If not, please join our [https://groups.google.com/forum/embed/?place=forum/minimac4-help&umich.edu| mailing list] to get updates about future releases or report possible bugs or email them to [mailto:yukt@umich.edu Ketian Yu] or [mailto:sayantan@umich.edu Sayantan Das].'''
= Download =
= Installation =
'''Minimac4 (version 1.0.0, released 2.14.2018)''' is currently available for download. Commonly used reference panels in <font face=Courier>M3VCF</font> format are available for download in [[#Reference Panels for Download | Reference Panels]].
'''Minimac4 (version 1.0.0, released 2.14.2018)''' is currently available on [https://github.com/Santy-8128/Minimac4 Minimac4 Github].
The easiest way to install Minimac4 and its dependencies is to use the install.sh file provided.
git clone <nowiki>https://github.com/statgen/Minimac4.git</nowiki>
cd Minimac4
bash install.sh
Please see [https://github.com/Santy-8128/Minimac4 Minimac4 Github] for the full instructions for installation.
Commonly used reference panels in <font face=Courier>M3VCF</font> format are available for download in [[#Reference Panels for Download | Reference Panels]].
= What's New =
= What's New =
The input file format, output file formats and typical command lines are same in Minimac4 (as they were in minimac3). Some of the main new features are summarized below:
The input file format, output file formats and typical command lines are the same in Minimac4 (as they were in minimac3). Some of the main new features are summarized below:
* '''Improved Speed - ''' Minimac4 is approximately '''6 times''' faster for 1000 Genomes Phase 1 and Phase 3 and '''2 times''' faster for the HRC reference panels at comparable accuracy (details of accuracy for imputing into 10 European samples are given here). The speed can be further improved by tuning the approximation parameters (see below), but we recommend using the default values.
* '''Improved Speed - ''' Minimac4 is approximately '''6 times''' faster for 1000 Genomes Phase 1 and Phase 3 and '''2 times''' faster for the HRC reference panels at comparable accuracy (details of accuracy for imputing into 10 European samples are given here). The speed can be further improved by tuning the approximation parameters (see below), but we recommend using the default values.
** Currently Minimac4 can ONLY handle M3VCF format files. If your reference panel is in VCF format, please use [[Minimac3]] to convert the VCF file to M3VCF (along with parameter estimation) and then use that M3VCF for imputation using Minimac4. The same holds for the option <code>--processReference</code> as well. Although the handle is made available, we will implement it in a later version.
** Currently Minimac4 can ONLY handle M3VCF format files. If your reference panel is in VCF format, please use [[Minimac3]] to convert the VCF file to M3VCF (along with parameter estimation) and then use that M3VCF for imputation using Minimac4. The same holds for the option <code>--processReference</code> as well. Although the handle is made available, we will implement it in a later version.
** Parameters such as <code>--rounds</code>, <code>--states</code>, <code>--rec</code>, <code>--err</code> have been deactivated for now until we implement parameter estimation in minimac4.
** Parameters such as <code>--rounds</code>, <code>--states</code>, <code>--rec</code>, <code>--err</code> have been deactivated for now until we implement parameter estimation in minimac4.
= Usage =
A typical Minimac4 command line for imputation is as follows
minimac4 --refHaps refPanel.m3vcf \
--haps targetStudy.vcf \
--prefix testRun
Here <font face=Courier>refPanel.m3vcf</font> is the reference panel used in M3VCF format (e.g. 1000 Genomes), <font face=Courier>targetStudy.vcf</font> is the phased GWAS data in VCF format, and <font face=Courier>testRun</font> is the prefix for the output files.
=== Full List of Options ===
Please see '''[[Minimac4 Documentation]]''' for detailed explanation of all available options.
Also, users can always type the following for the full list of available options:
minimac4 --help
=== Convert VCF to M3VCF ===
If the reference panel is in VCF format, please use [[Minimac3]] to convert it into M3VCF format first.
../bin/Minimac3 --refHaps refPanel.vcf \
--processReference \
--prefix refPanel
=== Multi-Threading ===
The following example shows the same analysis as above, but using 5 threads:
minimac4 --refHaps refPanel.m3vcf \
--haps targetStudy.vcf \
--prefix testRun \
--cpus 5
= Reference Panels for Download =
= Reference Panels for Download =
| [ftp://share.sph.umich.edu/minimac3/G1K_P1_CHR_X_VCF_M3VCF_FILES.tar.gz Download] <!--[ftp://share.sph.umich.edu/minimac3/G1K_P1_CHR_X_VCF_M3VCF_FILES.tar.gz Download]-->
| [ftp://share.sph.umich.edu/minimac3/G1K_P1_CHR_X_VCF_M3VCF_FILES.tar.gz Download] <!--[ftp://share.sph.umich.edu/minimac3/G1K_P1_CHR_X_VCF_M3VCF_FILES.tar.gz Download]-->
|}
|}
= Useful Wiki Pages =
There are a few pages in this Wiki that may be useful to for '''Minimac4''' users. Here are links to a few:
* [[Minimac4| Minimac4 Overview Page]]
* [[Minimac4 Documentation]]
* [[M3VCF Files| M3VCF Files]]
