Difference between revisions of "Minimac4"

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(Created page with " = Introduction = '''Minimac4 ''' is a latest version in the series of imputation software (preceded by Minimac3, Minimac2 and minimac. ...")
 
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= Introduction =
 
= Introduction =
  
'''Minimac4 ''' is a latest version in the series of imputation software (preceded by [[Minimac3|Minimac3]], [[Minimac2|Minimac2]] and [[Minimac|minimac]].
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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 negligible fall in imputation quality.
  
lower memory and more computationally efficient implementation of the genotype imputation algorithms in . '''Minimac3''' is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. It accomplishes this by identifying repeat haplotype patterns and using these to simplify the underlying calculations, with no loss of accuracy.
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= Download =
  
Minimac3 uses [[M3VCF Files|<font face=Courier>M3VCF</font> files]] (customized minimac3 VCF files) to store reference panel information in a compact form, thus saving on memory and time required to read large datasets. Users can use Minimac3 to convert standard VCF files to <font face=Courier>M3VCF</font> files. <font face=Courier>M3VCF</font> files can also store pre-calculated estimates of recombination fraction and error, which speeds up later rounds of imputationMinimac3 outputs results in the form of standard VCF files for easy data manipulation in downstream analysis.
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'''Minimac4 ''' is currently available for testing purposes only. Commonly used reference panels in <font face=Courier>M3VCF</font> format are available for download in [[#Reference Panels for Download | Reference Panels]].
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The Minimac3 mailing list has been renamed as the [https://groups.google.com/forum/embed/?place=forum/minimac4-help&umich.edu| 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].'''
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'''VERSION: 1.0.1 !!! (Updated 12.1.2016) !!!'''
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'''Github Repo:''' Users can clone from github repository as well : [https://github.com/Santy-8128/Minimac4 Minimac4 Github]
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'''Cloning from GitHub is recommened so that updates can be easily pulled back !!!'''

Revision as of 20:59, 1 December 2016

Introduction

Minimac4 is a latest version in the series of genotype imputation software - [preceded by Minimac3 (2015), Minimac2 (2014), minimac (2012) and MaCH (2010). Minimac4 is a lower memory and more computationally efficient implementation of the original algorithms with negligible fall in imputation quality.

Download

Minimac4 is currently available for testing purposes only. Commonly used reference panels in M3VCF format are available for download in Reference Panels.

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 mailing list to get updates about future releases or report possible bugs or email them to Sayantan Das.

VERSION: 1.0.1 !!! (Updated 12.1.2016) !!!

Github Repo: Users can clone from github repository as well : Minimac4 Github

Cloning from GitHub is recommened so that updates can be easily pulled back !!!