Minimac4 - Revision history

Lefaivej at 15:40, 14 June 2023

2023-06-14T15:40:41Z

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			= IMPORTANT NOTE !!! =

			This wiki is outdated and only applicable to version 4.0.x (a.k.a 1.0.x). Documentation for version 4.1.x can be found on the [https://github.com/Santy-8128/Minimac4 Minimac4 Github page].

	= Introduction =		= Introduction =

Abought: Add category tag to improve findability

2022-10-18T18:10:54Z

Add category tag to improve findability

← Older revision		Revision as of 14:10, 18 October 2022
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	* [[M3VCF Files\| M3VCF Files]]		* [[M3VCF Files\| M3VCF Files]]

			[[Category:Software]]

Yukt at 03:29, 20 July 2019

2019-07-20T03:29:04Z

← Older revision		Revision as of 23:29, 19 July 2019
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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

Yukt: /* Full List of Options */

2019-07-20T03:22:21Z

Full List of Options

← Older revision		Revision as of 23:22, 19 July 2019
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	=== Full List of Options ===		=== Full List of Options ===
	~~Users~~ can always type the following for ~~further support~~:		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		minimac4 --help

	~~'''Please see [[Minimac4 Documentation \| Minimac4 Documentation]] for detailed explanation of all available options.'''~~

	=== Convert VCF to M3VCF ===		=== Convert VCF to M3VCF ===

Yukt: /* Usage */

2019-07-20T03:14:56Z

Usage

← Older revision		Revision as of 23:14, 19 July 2019
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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.

			=== 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.'''

	=== Convert VCF to M3VCF ===		=== Convert VCF to M3VCF ===
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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 =

Yukt at 03:13, 20 July 2019

2019-07-20T03:13:58Z

← Older revision		Revision as of 23:13, 19 July 2019
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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]]

Yukt: /* Usage */

2019-07-20T03:10:48Z

Usage

← Older revision		Revision as of 23:10, 19 July 2019
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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.		=== 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 \

Yukt: /* Usage */

2019-07-20T03:09:33Z

Usage

← Older revision		Revision as of 23:09, 19 July 2019
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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.
			../bin/Minimac3 --refHaps refPanel.vcf \
			--processReference \
			--prefix refPanel

	=== Multi-Threading ===		=== Multi-Threading ===

Yukt: /* Usage */

2019-07-20T03:02:57Z

Usage

← Older revision		Revision as of 23:02, 19 July 2019
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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.

			=== Multi-Threading ===
			The following example shows the same analysis as above, but using 5 threads:

			minimac4 --refHaps refPanel.m3vcf \
			--haps targetStudy.vcf \
			--prefix testRun \
			--cpus 5

			=== Full List of Options ===
	Users can always type the following for further support:		Users can always type the following for further support:
	minimac4 --help		minimac4 --help

Yukt at 22:30, 16 July 2019

2019-07-16T22:30:35Z

← Older revision		Revision as of 18:30, 16 July 2019
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	minimac4 --help		minimac4 --help

	'''Please see [[Minimac4 Documentation \| ~~Minimac3~~ Documentation]] for detailed explanation of all available options.'''		'''Please see [[Minimac4 Documentation \| Minimac4 Documentation]] for detailed explanation of all available options.'''

	= Reference Panels for Download =		= Reference Panels for Download =