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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 = |
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| * [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''') | | * [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''') |
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| + | * [[Minimac3 Cookbook : Chromosome X Imputation| Chromosome X Imputation]] |
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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 ]] |
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| * [[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 [[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].''' |
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− | {| class="wikitable" border="1" cellpadding="2" | + | '''VERSION: 2.0.1 !!! (Updated 6.6.2016) !!!''' |
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| + | '''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)
| |
− | | [[Media : Minimac3.v1.0.0.binary-OMP.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].. |
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| = 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 | + | ## DOWNLOAD, EXTRACT MINIMAC3 AND COMPILE |
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− | 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 |
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| /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] |
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| = 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]] |