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760 bytes added, 16:52, 16 July 2019
Usage added. Full documentation will be on a separate page.
= Download =
'''Minimac4 (version 1.0.0, released 2.14.2018)''' is currently available for downloadon [https://github. Commonly used reference panels in <font face=Courier>M3VCF<com/Santy-8128/font> format are available for download Minimac4 Minimac4 Github]. Please follow the instructions in [[#Reference Panels the GitHub repository for Download | Reference Panels]]installation.
'''Github Repo:''' : Commonly used reference panels in <font face=Courier>M3VCF</font> format are available for download in [https://github[#Reference Panels for Download | Reference Panels]].com/Santy-8128/Minimac4 Minimac4 Github]
= What's New =
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.
** 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.
= Usage =
The easiest way to install Minimac4 and its dependencies is to use the file provided.
git clone <nowiki></nowiki>
cd Minimac4
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.
Users can always type the following for further support:
minimac4 --help
= Reference Panels for Download =

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