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Minimac3 (view source)

Revision as of 15:40, 18 October 2022

1,761 bytes added ,  15:40, 18 October 2022
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* '''New Version [[Minimac4]] available ! Please Check out !!!'''
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* '''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/minimac4-help#!forum/minimac4-help mailing list] to get updates about future releases, bug fixes or post queries.'''
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* '''No further development on Minimac3 !!!''' See [[Minimac3 ChangeLog | ChangeLog ]] for details !!!
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= Useful Wiki Pages =
 
= Useful Wiki Pages =
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* [[Minimac3 Examples| Minimac3 Examples]]
 
* [[Minimac3 Examples| Minimac3 Examples]]
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* [[Minimac3 Info File| Minimac3 Info File]]
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* [[Minimac3 ChangeLog | Minimac3 ChangeLog ]]
    
* [[M3VCF Files| M3VCF Files]]
 
* [[M3VCF Files| M3VCF Files]]
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= Download =
 
= Download =
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'''Minimac3 ''' is currently available as a pre-release release version. Commonly used reference panels in <font face=Courier>M3VCF</font> format are available for download in [[#Reference Panels for Download | Reference Panels]]. The authors would really appreciate if users report possible bugs by e-mailing [mailto:sayantan@umich.edu Sayantan Das].
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'''Minimac3 ''' is currently available as a release version. 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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'''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/minimac4-help#!forum/minimac4-help 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: 2.0.1 !!! (Updated 6.6.2016) !!!'''
    
'''Github Repo:''' Users can clone from github repository as well : [https://github.com/Santy-8128/Minimac3 Minimac3 Github]  
 
'''Github Repo:''' Users can clone from github repository as well : [https://github.com/Santy-8128/Minimac3 Minimac3 Github]  
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'''Cloning from GitHub is recommened so that updates can be easily pulled back !!!'''
    
{| class="wikitable"  style="text-align:center"  border="1" cellpadding="2"
 
{| class="wikitable"  style="text-align:center"  border="1" cellpadding="2"
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! Download Link
 
! Download Link
 
|-  
 
|-  
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| Minimac3 Source Files
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| Source Files  
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| [ftp://share.sph.umich.edu/minimac3/Minimac3.v1.tar.gz UNIX Users ]
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| [ftp://share.sph.umich.edu/minimac3/Minimac3.v2.0.1.tar.gz UNIX Users ]
 
|-  
 
|-  
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| Minimac3 Executable  
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| Binary Executable <sup>&#8224;</sup>
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| [ftp://share.sph.umich.edu/minimac3/Minimac3.v1.binary.tar.gz UNIX Users ]
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| [ftp://share.sph.umich.edu/minimac3/Minimac3Executable.tar.gz UNIX Users ]
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|-
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|}
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| Minimac3-omp Executable <br>(for parallel computing)
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|  [ftp://share.sph.umich.edu/minimac3/Minimac3.v1.binary-OMP.tar.gz UNIX Users ]
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|}
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'''<sup>&#8224;</sup>''' Binary executables are NOT guaranteed to run on every LINUX machine. Please compile from source files if you have trouble with the executable, or else contact the author [mailto:sayantan@umich.edu Sayantan Das]..
    
= Usage=
 
= Usage=
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Users should follow the following steps to compile '''Minimac3''' (if they downloaded the source files) or should skip them (if they downloaded the binary executable).
 
Users should follow the following steps to compile '''Minimac3''' (if they downloaded the source files) or should skip them (if they downloaded the binary executable).
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  ## EXTRACT MINIMAC3 AND COMPILE
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  ## DOWNLOAD, EXTRACT MINIMAC3 AND COMPILE
 
  &nbsp;
 
  &nbsp;
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  tar -xzvf Minimac3.v1.0.0.tar.gz
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wget ftp://share.sph.umich.edu/minimac3/Minimac3.v2.0.1.tar.gz
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  tar -xzvf Minimac3.v2.0.1.tar.gz
 
  cd Minimac3/
 
  cd Minimac3/
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  make ## Type 'make openmp' to compile multi-thread binary
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  make
    
A typical '''Minimac3''' command line for imputation is as follows  
 
A typical '''Minimac3''' command line for imputation is as follows  
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Some commonly used reference panels are available for download here:
 
Some commonly used reference panels are available for download here:
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'''Chr X Haplotypes for 1000 Genomes Phase 3 have been updated on Oct 20 to include multi-allelic variants as well (split as bi-allelic variants) !!!'''
    
{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
 
{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
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| -
 
| -
 
| 1-22,X
 
| 1-22,X
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| [ftp://share.sph.umich.edu/minimac3/G1K_P3_VCF_Files.tar.gz Download]
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| [ftp://share.sph.umich.edu/minimac3/G1K_P3_VCF_Files.tar.gz Download] <!--[ftp://share.sph.umich.edu/minimac3/G1K_P3_VCF_Files.tar.gz Download]-->
 
|-  
 
|-  
 
| rowspan=2  style="text-align:center" | '''M3VCF'''
 
| rowspan=2  style="text-align:center" | '''M3VCF'''
 
| YES
 
| YES
 
| 1-22,X
 
| 1-22,X
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|  [ftp://share.sph.umich.edu/minimac3/G1K_P3_M3VCF_FILES_WITH_ESTIMATES.tar.gz Download]
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|  [ftp://share.sph.umich.edu/minimac3/G1K_P3_M3VCF_FILES_WITH_ESTIMATES.tar.gz Download] <!-- [ftp://share.sph.umich.edu/minimac3/G1K_P3_M3VCF_FILES_WITH_ESTIMATES.tar.gz Download]-->
 
|-  
 
|-  
 
|NO
 
|NO
 
| 1-22,X
 
| 1-22,X
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| [ftp://share.sph.umich.edu/minimac3/G1K_P3_M3VCF_FILES_NO_ESTIMATES.tar.gz Download]
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| [ftp://share.sph.umich.edu/minimac3/G1K_P3_M3VCF_FILES_NO_ESTIMATES.tar.gz Download] <!--[ftp://share.sph.umich.edu/minimac3/G1K_P3_M3VCF_FILES_NO_ESTIMATES.tar.gz Download]-->
 
|-  
 
|-  
 
| '''VCF''','''M3VCF'''
 
| '''VCF''','''M3VCF'''
 
| YES
 
| YES
 
| X
 
| X
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| [ftp://share.sph.umich.edu/minimac3/G1K_P3_CHR_X_VCF_M3VCF_FILES.tar.gz Download]
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| [ftp://share.sph.umich.edu/minimac3/G1K_P3_CHR_X_VCF_M3VCF_FILES.tar.gz Download] <!--[ftp://share.sph.umich.edu/minimac3/G1K_P3_CHR_X_VCF_M3VCF_FILES.tar.gz Download]-->
 
|-  
 
|-  
 
| rowspan=4 |  '''1000 Genomes''' <br>
 
| rowspan=4 |  '''1000 Genomes''' <br>
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| YES
 
| YES
 
| X
 
| X
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| [ftp://share.sph.umich.edu/minimac3/G1K_P1_CHR_X_VCF_M3VCF_FILES.tar.gz Download]
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| [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]-->
 
|}
 
|}
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= Reference =
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If you use [[minimac3]] please cite:
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''Das S, Forer L, Schönherr S, Sidore C, Locke AE'' et al. Next-generation genotype imputation service and methods. Nature Genetics 2016; 48, 1284–1287 (2016) doi:10.1038/ng.3656[http://www.nature.com/ng/journal/v48/n10/full/ng.3656.html]
    
= Contact =
 
= Contact =
    
In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].
 
In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].
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[[Category:Software]]
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