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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.'''
* '''No further development on Minimac3 !!!''' See [[Minimac3 ChangeLog | ChangeLog ]] for details !!!
= Useful Wiki Pages =
= Useful Wiki Pages =
There are a few pages in this Wiki that may be useful to for '''Minimac3''' users. Here are links to a few:
There are a few pages in this Wiki that may be useful to for '''Minimac3''' users. Here are links to a few:
* [[Minimac3 | Minimac3 Overview Page]]
* [[Minimac3| Minimac3 Overview Page]]
* [[Minimac3 Usage | Minimac3 Usage and Documentation]]
* [[Minimac3 Usage | Minimac3 Usage and Documentation]]
* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')
* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')
* [[Minimac3 Cookbook : Chromosome X Imputation| Chromosome X Imputation]]
* [[Minimac3 Examples| Minimac3 Examples]]
* [[Minimac3 Examples| Minimac3 Examples]]
* [[Minimac3 Info File| Minimac3 Info File]]
* [[Minimac3 ChangeLog | Minimac3 ChangeLog ]]
* [[M3VCF Files| M3VCF Files]]
* [[M3VCF Files| M3VCF Files]]
= Introduction =
= Introduction =
'''Minimac3 ''' is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in [[Minimac|minimac]] and [[Minimac2|Minimac2]]. '''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.
'''Minimac3 ''' is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in [[Minimac|minimac]] and [[Minimac2|minimac2]]. '''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.
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 imputation. Minimac3 outputs results in the form of standard VCF files for easy data manipulation in downstream analysis.
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 imputation. Minimac3 outputs results in the form of standard VCF files for easy data manipulation in downstream analysis.
= Download =
= Download =
'''Minimac3 ''' is currently available as a pre-release release version. Commonly used reference panels in <code>M3VCF</code> format are available for download in [[Minimac3 Imputation Cookbook#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]].
'''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/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].'''
{| class="wikitable" border="1" cellpadding="2"
'''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]
'''Cloning from GitHub is recommened so that updates can be easily pulled back !!!'''
{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
|- bgcolor="lightgray"
|- bgcolor="lightgray"
! Description
! Description
! Download Link
! Download Link
|-
|-
| Minimac3 Executable
| Source Files
| [[Media : Minimac3.v1.0.0.binary.tar.gz | UNIX Users ]]
| [ftp://share.sph.umich.edu/minimac3/Minimac3.v2.0.1.tar.gz UNIX Users ]
|-
|-
| Minimac3 Source Files
| Binary Executable <sup>†</sup>
| [[Media : Minimac3.v1.0.0.tar.gz | UNIX Users ]]
| [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.v1.0.0.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
--prefix testRun
--prefix testRun
Here <code>refPanel.vcf</code> is the reference panel used in VCF format (e.g. 1000 Genomes), <code>targetStudy.vcf</code> is the phased GWAS data in VCF format, and <code>testRun</code> is the prefix for the output files. Some commonly used reference panels are available for download in [[Minimac3 Imputation Cookbook#Reference Panels for Download| Reference Panels]]. See wiki page on [[Minimac3 Usage| Detailed Usage]] and [[Minimac3 Imputation Cookbook|Imputation Cookbook]] for further details on using '''Minimac3''' for imputation analysis.
Here <font face=Courier>refPanel.vcf</font> is the reference panel used in VCF format (e.g. 1000 Genomes), <font face=Courier>targetStudy.vcf</font> is the phased GWAS data in VCF format, and <font face=Courier>testRun</font> is the prefix for the output files. Some commonly used reference panels are available for download in [[Minimac3 Imputation Cookbook#Reference Panels for Download| Reference Panels]]. See wiki page on [[Minimac3 Usage| Detailed Usage]] and [[Minimac3 Imputation Cookbook|Imputation Cookbook]] for further details on using '''Minimac3''' for imputation analysis.
Users can always type the following for further support:
Users can always type the following for further support:
/bin/Minimac3 --help
/bin/Minimac3 --help
= Reference Panels for Download =
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"
|- bgcolor="lightgray"
! width="150px" |Reference Panel
! width="100px" |Number <br> of Samples
! width="100px" |File Format
! width="100px" |Parameter <br> Estimates <br> Available
! width="120px" |Chromosomes
! width="80px" |Link
|-
| rowspan=4 | '''1000 Genomes''' <br>
'''Phase 3''' <br>
(version 5)
| rowspan=4 style="text-align:center" | '''2,504'''
| '''VCF'''
| -
| 1-22,X
| [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'''
| YES
| 1-22,X
| [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
| 1-22,X
| [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'''
| YES
| X
| [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>
'''Phase 1''' <br>
(version 3)
| rowspan=4 | '''1,092'''
| '''VCF'''
| -
| 1-22,X
| [ftp://share.sph.umich.edu/minimac3/G1K_P1_VCF_Files.tar.gz Download]
|-
| rowspan=2 style="text-align:center" | '''M3VCF'''
| YES
| 1-22,X
| [ftp://share.sph.umich.edu/minimac3/G1K_P1_M3VCF_FILES_WITH_ESTIMATES.tar.gz Download]
|-
| NO
| 1-22,X
| [ftp://share.sph.umich.edu/minimac3/G1K_P1_M3VCF_FILES_NO_ESTIMATES.tar.gz Download]
|-
| '''VCF''','''M3VCF'''
| YES
| X
| [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].
[[Category:Software]]
