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| The Minimac3 mailing list has been renamed as the Minimac4 mailing list. If you were already a member, no need to re-join. If not, please join our [https://groups.google.com/forum/embed/?place=forum/minimac4-help&umich.edu| mailing list] to get updates about future releases or report possible bugs or email them to [mailto:yukt@umich.edu Ketian Yu] or [mailto:sayantan@umich.edu Sayantan Das].''' | | The Minimac3 mailing list has been renamed as the Minimac4 mailing list. If you were already a member, no need to re-join. If not, please join our [https://groups.google.com/forum/embed/?place=forum/minimac4-help&umich.edu| mailing list] to get updates about future releases or report possible bugs or email them to [mailto:yukt@umich.edu Ketian Yu] or [mailto:sayantan@umich.edu Sayantan Das].''' |
| | | |
− | = Download = | + | = Installation = |
| | | |
− | '''Minimac4 (version 1.0.0, released 2.14.2018)''' is currently available on [https://github.com/Santy-8128/Minimac4 Minimac4 Github]. Please follow the instructions in the GitHub repository for installation. | + | '''Minimac4 (version 1.0.0, released 2.14.2018)''' is currently available on [https://github.com/Santy-8128/Minimac4 Minimac4 Github]. |
| + | |
| + | The easiest way to install Minimac4 and its dependencies is to use the install.sh file provided. |
| + | git clone <nowiki>https://github.com/statgen/Minimac4.git</nowiki> |
| + | cd Minimac4 |
| + | bash install.sh |
| + | |
| + | Please see [https://github.com/Santy-8128/Minimac4 Minimac4 Github] for the full instructions for installation. |
| | | |
| Commonly used reference panels in <font face=Courier>M3VCF</font> format are available for download in [[#Reference Panels for Download | Reference Panels]]. | | 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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| = Usage = | | = Usage = |
− | The easiest way to install Minimac4 and its dependencies is to use the install.sh file provided.
| |
− | git clone <nowiki>https://github.com/statgen/Minimac4.git</nowiki>
| |
− | cd Minimac4
| |
− | bash install.sh
| |
− |
| |
| A typical Minimac4 command line for imputation is as follows | | A typical Minimac4 command line for imputation is as follows |
| | | |
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| Here <font face=Courier>refPanel.m3vcf</font> is the reference panel used in M3VCF 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. | | Here <font face=Courier>refPanel.m3vcf</font> is the reference panel used in M3VCF 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. |
| | | |
− | If the reference panel is in VCF format, please use Minimac3 to convert it into M3VCF format first. | + | === Full List of Options === |
| + | Please see '''[[Minimac4 Documentation]]''' for detailed explanation of all available options. |
| + | |
| + | Also, users can always type the following for the full list of available options: |
| + | minimac4 --help |
| + | |
| + | === Convert VCF to M3VCF === |
| + | If the reference panel is in VCF format, please use [[Minimac3]] to convert it into M3VCF format first. |
| ../bin/Minimac3 --refHaps refPanel.vcf \ | | ../bin/Minimac3 --refHaps refPanel.vcf \ |
| --processReference \ | | --processReference \ |
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| --prefix testRun \ | | --prefix testRun \ |
| --cpus 5 | | --cpus 5 |
− |
| |
− | === Full List of Options ===
| |
− | Users can always type the following for further support:
| |
− | minimac4 --help
| |
− |
| |
− | '''Please see [[Minimac4 Documentation | Minimac4 Documentation]] for detailed explanation of all available options.'''
| |
| | | |
| = Reference Panels for Download = | | = Reference Panels for 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]--> | | | [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]--> |
| |} | | |} |
| + | |
| + | |
| + | = Useful Wiki Pages = |
| + | |
| + | There are a few pages in this Wiki that may be useful to for '''Minimac4''' users. Here are links to a few: |
| + | |
| + | * [[Minimac4| Minimac4 Overview Page]] |
| + | |
| + | * [[Minimac4 Documentation]] |
| + | |
| + | * [[M3VCF Files| M3VCF Files]] |