= Introduction =
'''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
negligible fall in 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]].
'''Github Repo:''' : [https://github.com/Santy-8128/Minimac4 Minimac4 Github]
= 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:
Automated Chunking - ''' Minimac4 automatically chunks the whole chromosome (into overlapping chunks), analyzes each chunk sequentially and then concatenates the imputed chunks back. This caps the memory usage across different chromosomes ( larger chromosomes need the same amount of memory as smaller ones). The length of the chunk and the overlap can be controlled by the parameters <code>--chunkLengthMb</code> and <code>--chunkLengthOverlapMb</code>, although we recommend using the default values.
* '''Approximations - ''' Minimac4 uses some simple approximations to speed up the imputation analyses. The levels of approximation can be controlled by the parameters <code>--probThreshold</code>, <code>--diffThreshold</code>, and <code>--topThreshold</code> (details given in Minimac4 Usage). Higher levels of approximation will reduce the compute time but
also marginally reduce the imputation accuracy. We recommend using the default values .
* '''Other Helpful Features'''
** We introduced a
parameter <code>--memUsage</code> that will estimate and report the memory required by the imputation experiment. This feature should be useful for users running their jobs on a compute cluster that requires memory specification.** We introduced some other FORMAT options for the output dosage data which should be sufficient to enable users to retrieve haplotype dosages, genotype probabilities, genotype dosages or any other measure of summary that they want.
= 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]-->