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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.
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:firstname.lastname@example.org Sayantan Das].'''
'''Minimac4 (version 1.0.2
, updated 6. 29. 2017)''' is currently available for testing purposes only (while we still run more tests and wait on feedback about potential bugs). 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 =
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:
* '''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.
* '''Obsolete Features'''
** In Minimac4, we removed the <code>--doseOutput</code> and <code>--hapOutput</code> options. Please use [[DosageConvertor]] to convert your files to MaCH or PLINK dosage format.
** 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.
= 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]-->