32
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchAdd category tag to improve findability
* '''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 =
* [[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]]
= Download =
= Download =
'''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].
'''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]].
{| class="wikitable" border="1" cellpadding="2"
'''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: 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-omp Executable (for parallel computing)
| Binary Executable <sup>†</sup>
| [[Media : Minimac3.v1.0.0.binary-OMP.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
= Reference Panels for Download =
= Reference Panels for Download =
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"
|- bgcolor="lightgray"
|- bgcolor="lightgray"
! Reference Panel
! width="150px" |Reference Panel
! Number of Samples
! width="100px" |Number <br> of Samples
! Description
! width="100px" |File Format
! Download Link
! width="100px" |Parameter <br> Estimates <br> Available
! width="120px" |Chromosomes
! width="80px" |Link
|-
|-
| rowspan=4 | '''1000 Genomes Phase 3'''
| rowspan=4 | '''1000 Genomes''' <br>
| rowspan=4 style="text-align:center" | '''2,534'''
'''Phase 3''' <br>
| GzVCF Format on Chr 1-22,X
(version 5)
| Coming Soon
| 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]-->
|-
|-
| M3VCF Format (With Parameter Estimates) on Chr 1-22,X
| rowspan=2 style="text-align:center" | '''M3VCF'''
| Coming Soon
| 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]-->
|-
|-
| M3VCF Format (Without Parameter Estimates) on Chr 1-22,X
|NO
| Coming Soon
| 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]-->
|-
|-
| Only Chr X (VCF and M3VCF format)
| '''VCF''','''M3VCF'''
| Coming Soon
| 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 Phase 1'''
| rowspan=4 | '''1000 Genomes''' <br>
'''Phase 1''' <br>
(version 3)
| rowspan=4 | '''1,092'''
| rowspan=4 | '''1,092'''
| VCF Files
| '''VCF'''
| Coming Soon
| -
| 1-22,X
| [ftp://share.sph.umich.edu/minimac3/G1K_P1_VCF_Files.tar.gz Download]
|-
|-
| M3VCF Format (With Parameter Estimates) on Chr 1-22,X
| rowspan=2 style="text-align:center" | '''M3VCF'''
| Coming Soon
| YES
| 1-22,X
| [ftp://share.sph.umich.edu/minimac3/G1K_P1_M3VCF_FILES_WITH_ESTIMATES.tar.gz Download]
|-
|-
| M3VCF Format (Without Parameter Estimates) on Chr 1-22,X
| NO
| Coming Soon
| 1-22,X
| [ftp://share.sph.umich.edu/minimac3/G1K_P1_M3VCF_FILES_NO_ESTIMATES.tar.gz Download]
|-
|-
| Only Chr X (VCF and M3VCF format)
| '''VCF''','''M3VCF'''
| Coming Soon
| 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]]
