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* '''New Version [[Minimac4]] available ! Please Check out !!!'''
* '''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.'''
* '''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/minimac3-help&umich.edu| mailing list] to get updates about future releases, bug fixes or post queries.'''
* '''No further development on Minimac3 !!!''' See [[Minimac3 ChangeLog | ChangeLog ]] for details !!!
= Useful Wiki Pages =
= Useful Wiki Pages =
'''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]].
'''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]].
'''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/minimac3-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].'''
'''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].'''
'''VERSION: 1.0.13 !!! (Updated 10.15.2015) !!!'''
'''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]
! Download Link
! Download Link
|-
|-
| Minimac3 Source Files
| Source Files
| [ftp://share.sph.umich.edu/minimac3/Minimac3.v1.0.13.tar.gz UNIX Users ]
| [ftp://share.sph.umich.edu/minimac3/Minimac3.v2.0.1.tar.gz UNIX Users ]
|-
| Binary Executable <sup>†</sup>
| [ftp://share.sph.umich.edu/minimac3/Minimac3Executable.tar.gz UNIX Users ]
|}
'''<sup>†</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=
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).
## EXTRACT MINIMAC3 AND COMPILE
## DOWNLOAD, EXTRACT MINIMAC3 AND COMPILE
tar -xzvf Minimac3.v1.0.13.tar.gz
wget ftp://share.sph.umich.edu/minimac3/Minimac3.v2.0.1.tar.gz
tar -xzvf Minimac3.v2.0.1.tar.gz
cd Minimac3/
cd Minimac3/
make
make
Some commonly used reference panels are available for download here:
Some commonly used reference panels are available for download here:
'''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"
| [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]-->
| [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]-->
|}
|}
= Reference =
If you use [[minimac3]] please cite:
''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].
