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Minimac4

279 bytes added, 23:29, 19 July 2019
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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 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 follow see [https://github.com/Santy-8128/Minimac4 Minimac4 Github] for the full instructions in the GitHub repository for installation.
Commonly used reference panels in <font face=Courier>M3VCF</font> format are available for download in [[#Reference Panels for Download | Reference Panels]].
= Usage =
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
 
A typical Minimac4 command line for imputation is as follows
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 ===
--prefix testRun \
--cpus 5
 
=== Full List of Options ===
Users can always type the following for further support:
minimac4 --help
 
'''Please see [[Minimac4 Documentation | Minimac4 Documentation]] for detailed explanation of all available options.'''
= 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]-->
|}
 
 
= 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]]
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