Minimac3 Imputation Cookbook - Revision history

Santy.8128: /* Useful Wiki Pages */

2015-01-30T03:28:16Z

Useful Wiki Pages

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	* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')		* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')

			* [[Minimac3 Cookbook : Chromosome X Imputation \| Chromosome X Imputation ]]

	* [[Minimac3 Cookbook : Pre-Phasing \| Pre-Phasing ]]		* [[Minimac3 Cookbook : Pre-Phasing \| Pre-Phasing ]]

Santy.8128: /* Useful Wiki Pages */

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Useful Wiki Pages

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	* [[Minimac3 Usage \| Minimac3 Usage and Documentation]]		* [[Minimac3 Usage \| Minimac3 Usage and Documentation]]

			* [[Minimac3 - Full List of Options]]

	* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')		* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')

			* [[Minimac3 Cookbook : Pre-Phasing \| Pre-Phasing ]]

			* [[Minimac3 Cookbook : Converting Files to VCF\| Converting Files to VCF]]

	* [[Minimac3 Examples\| Minimac3 Examples]]		* [[Minimac3 Examples\| Minimac3 Examples]]

Goncalo: /* Download */

2015-01-30T03:15:02Z

Download

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	= Download =		= Download =

	'''Minimac3 ''' is available as ~~an undocumented~~ release ~~version~~. The source files (and binary executable) are available for download in [[Minimac3#Download \| Source Files]] and commonly used reference panels in VCF and <font face=Courier>M3VCF</font> formats are available for download in [[Minimac3#Reference Panels for Download \| Reference Panels]].		'''Minimac3 ''' is currently available as a pre-release. The source files (and binary executable) are available for download in [[Minimac3#Download \| Source Files]] and commonly used reference panels in VCF and <font face=Courier>M3VCF</font> formats are available for download in [[Minimac3#Reference Panels for Download \| Reference Panels]].

	= Useful Wiki Pages =		= Useful Wiki Pages =

Goncalo: /* Download Reference Panel */

2015-01-30T03:14:16Z

Download Reference Panel

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	== Download Reference Panel ==		== Download Reference Panel ==

	Commonly used reference panels are 1000 Genomes Phase 3 (2,535 samples), 1000 Genomes Phase 1 (1,094 samples), HapMap2 (269 samples), Haplotype Reference Consortium (32,914 samples) etc. Users are advised to use either 1000 Genomes Phase 3 ~~(available for download in [[#Reference Panels for Download \|Reference Panels ]])~~ or the Haplotype Reference Consortium (which due to data privacy issues cannot be shared publicly but can be used for imputation remotely on a server through a [http://imputationserver.sph.umich.edu/ imputation server] setup at University of Michigan). Reference panels for different versions of 1000 Genomes, in both VCF and <code>M3VCF</code> format, are available for download in [[Minimac3#Reference Panels for Download \|Reference Panels]].		Commonly used reference panels are 1000 Genomes Phase 3 (2,535 samples), 1000 Genomes Phase 1 (1,094 samples), HapMap2 (269 samples), Haplotype Reference Consortium (32,914 samples) etc. Users are advised to use either 1000 Genomes Phase 3 or the Haplotype Reference Consortium (which due to data privacy issues cannot be shared publicly but can be used for imputation remotely on a server through a [http://imputationserver.sph.umich.edu/ imputation server] setup at University of Michigan). Reference panels for different versions of 1000 Genomes, in both VCF and <code>M3VCF</code> format, are available for download in [[Minimac3#Reference Panels for Download \|Reference Panels]].

	== Impute Samples ==		== Impute Samples ==

Santy.8128: /* Chromosome X Imputation */

2015-01-30T02:00:34Z

Chromosome X Imputation

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	Chromosome X has a pseudo-autosomal region (PAR) which can be imputed for males and females together. Imputing the PAR on chromosome X is same as usual imputation, since both males and females are diploids at these sites. However, the non pseudo-autosomal region needs to be imputed for males and females separately, as males are haploids while females are diploids. Of course, the PAR and non-PAR regions need to be imputed separately. See our wiki page on [[Minimac3 Cookbook : Chromosome X Imputation \|Chromosome X Imputation]] for details on imputing chromosome X.		Chromosome X has a pseudo-autosomal region (PAR) which can be imputed for males and females together. Imputing the PAR on chromosome X is same as usual imputation, since both males and females are diploids at these sites. However, the non pseudo-autosomal region needs to be imputed for males and females separately, as males are haploids while females are diploids. Of course, the PAR and non-PAR regions need to be imputed separately. See our wiki page on [[Minimac3 Cookbook : Chromosome X Imputation \|Chromosome X Imputation]] for details on imputing chromosome X.

	~~The following example illustrates imputation on the non-PAR of chromosome X for males and females separately (files available in <code>Minimac3/test/</code> directory)~~

	~~Male Samples (Non-PAR)~~
	~~../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.males.vcf --prefix testRun~~

	~~Female Samples (Non-PAR)~~
	~~../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.females.vcf --prefix testRun~~

	NOTE: For imputing non-PAR of chromosome X, user must analyze male and female samples separately, otherwise program would crash. User should also ensure that the reference panel consists of only PAR or non-PAR region of chromosome X, otherwise program would crash.

	= Download =		= Download =

Santy.8128: /* Chromosome X Imputation */

2015-01-30T02:00:08Z

Chromosome X Imputation

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	= Chromosome X Imputation =		= Chromosome X Imputation =

	Chromosome X has a pseudo-autosomal region (PAR) which can be imputed for males and females together. Imputing the PAR on chromosome X is same as usual imputation, since both males and females are diploids at these sites. However, the non pseudo-autosomal region needs to be imputed for males and females separately, as males are haploids while females are diploids. Of course, the PAR and non-PAR regions need to be imputed separately.		Chromosome X has a pseudo-autosomal region (PAR) which can be imputed for males and females together. Imputing the PAR on chromosome X is same as usual imputation, since both males and females are diploids at these sites. However, the non pseudo-autosomal region needs to be imputed for males and females separately, as males are haploids while females are diploids. Of course, the PAR and non-PAR regions need to be imputed separately. See our wiki page on [[Minimac3 Cookbook : Chromosome X Imputation \|Chromosome X Imputation]] for details on imputing chromosome X.

	The following example illustrates imputation on the non-PAR of chromosome X for males and females separately (files available in <code>Minimac3/test/</code> directory)		The following example illustrates imputation on the non-PAR of chromosome X for males and females separately (files available in <code>Minimac3/test/</code> directory)

Santy.8128: /* Impute Samples */

2015-01-30T01:57:06Z

Impute Samples

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	== Impute Samples ==		== Impute Samples ==

	The final step for imputation involves running '''Minimac3''' to perform the imputation analysis. Now that we have the pre-phased GWAS panel (in VCF format) and the appropriate reference panel (in VCF or <code>M3VCF</code> format), we can run Minimac3 as follows. In the following examples, the first one uses a VCF file for reference (that can be obtained as explained above) and the second example uses a <code>M3VCF</code> file (that might have been downloaded from ~~the links~~ [[#Reference Panels for Download\|~~below~~]] or created on a previous run of Minimac3).		The final step for imputation involves running '''Minimac3''' to perform the imputation analysis. Now that we have the pre-phased GWAS panel (in VCF format) and the appropriate reference panel (in VCF or <code>M3VCF</code> format), we can run Minimac3 as follows. In the following examples, the first one uses a VCF file for reference (that can be obtained as explained above) and the second example uses a <code>M3VCF</code> file (that might have been downloaded from [[Minimac3#Reference Panels for Download\|Reference Panels]] or created on a previous run of Minimac3).

	../bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.vcf \		../bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.vcf \

Santy.8128: /* Impute Samples */

2015-01-30T01:56:27Z

Impute Samples

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	Commonly used reference panels are 1000 Genomes Phase 3 (2,535 samples), 1000 Genomes Phase 1 (1,094 samples), HapMap2 (269 samples), Haplotype Reference Consortium (32,914 samples) etc. Users are advised to use either 1000 Genomes Phase 3 (available for download in [[#Reference Panels for Download \|Reference Panels ]]) or the Haplotype Reference Consortium (which due to data privacy issues cannot be shared publicly but can be used for imputation remotely on a server through a [http://imputationserver.sph.umich.edu/ imputation server] setup at University of Michigan). Reference panels for different versions of 1000 Genomes, in both VCF and <code>M3VCF</code> format, are available for download in [[Minimac3#Reference Panels for Download \|Reference Panels]].		Commonly used reference panels are 1000 Genomes Phase 3 (2,535 samples), 1000 Genomes Phase 1 (1,094 samples), HapMap2 (269 samples), Haplotype Reference Consortium (32,914 samples) etc. Users are advised to use either 1000 Genomes Phase 3 (available for download in [[#Reference Panels for Download \|Reference Panels ]]) or the Haplotype Reference Consortium (which due to data privacy issues cannot be shared publicly but can be used for imputation remotely on a server through a [http://imputationserver.sph.umich.edu/ imputation server] setup at University of Michigan). Reference panels for different versions of 1000 Genomes, in both VCF and <code>M3VCF</code> format, are available for download in [[Minimac3#Reference Panels for Download \|Reference Panels]].

	=== Impute Samples ===		== Impute Samples ==

	The final step for imputation involves running '''Minimac3''' to perform the imputation analysis. Now that we have the pre-phased GWAS panel (in VCF format) and the appropriate reference panel (in VCF or <code>M3VCF</code> format), we can run Minimac3 as follows. In the following examples, the first one uses a VCF file for reference (that can be obtained as explained above) and the second example uses a <code>M3VCF</code> file (that might have been downloaded from the links [[#Reference Panels for Download\|below]] or created on a previous run of Minimac3).		The final step for imputation involves running '''Minimac3''' to perform the imputation analysis. Now that we have the pre-phased GWAS panel (in VCF format) and the appropriate reference panel (in VCF or <code>M3VCF</code> format), we can run Minimac3 as follows. In the following examples, the first one uses a VCF file for reference (that can be obtained as explained above) and the second example uses a <code>M3VCF</code> file (that might have been downloaded from the links [[#Reference Panels for Download\|below]] or created on a previous run of Minimac3).

Santy.8128: /* Convert Files to VCF */

2015-01-30T01:56:04Z

Convert Files to VCF

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	After the pre-phasing has been done, we can begin to run the imputation. But before that, we need to convert our phased GWAS panel files (obtained above) to VCF format (since Minimac3 can only use VCF format files). If pre-phased data is already available in VCF format, users can skip this step. Otherwise, see our wiki page on [[Minimac3 Cookbook : Converting Files to VCF\| Converting to VCF]] for further details/tools on converting files to VCF		After the pre-phasing has been done, we can begin to run the imputation. But before that, we need to convert our phased GWAS panel files (obtained above) to VCF format (since Minimac3 can only use VCF format files). If pre-phased data is already available in VCF format, users can skip this step. Otherwise, see our wiki page on [[Minimac3 Cookbook : Converting Files to VCF\| Converting to VCF]] for further details/tools on converting files to VCF


	== Download Reference Panel ==		== Download Reference Panel ==

Santy.8128: /* Download Reference Panel */

2015-01-30T01:55:55Z

Download Reference Panel

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	=== Download Reference Panel ===		== Download Reference Panel ==

	Commonly used reference panels are 1000 Genomes Phase 3 (2,535 samples), 1000 Genomes Phase 1 (1,094 samples), HapMap2 (269 samples), Haplotype Reference Consortium (32,914 samples) etc. Users are advised to use either 1000 Genomes Phase 3 (available for download in [[#Reference Panels for Download \|Reference Panels ]]) or the Haplotype Reference Consortium (which due to data privacy issues cannot be shared publicly but can be used for imputation remotely on a server through a [http://imputationserver.sph.umich.edu/ imputation server] setup at University of Michigan). Reference panels for different versions of 1000 Genomes, in both VCF and <code>M3VCF</code> format, are available for download in [[#Reference Panels for Download \|Reference Panels]].		Commonly used reference panels are 1000 Genomes Phase 3 (2,535 samples), 1000 Genomes Phase 1 (1,094 samples), HapMap2 (269 samples), Haplotype Reference Consortium (32,914 samples) etc. Users are advised to use either 1000 Genomes Phase 3 (available for download in [[#Reference Panels for Download \|Reference Panels ]]) or the Haplotype Reference Consortium (which due to data privacy issues cannot be shared publicly but can be used for imputation remotely on a server through a [http://imputationserver.sph.umich.edu/ imputation server] setup at University of Michigan). Reference panels for different versions of 1000 Genomes, in both VCF and <code>M3VCF</code> format, are available for download in [[Minimac3#Reference Panels for Download \|Reference Panels]].

	=== Impute Samples ===		=== Impute Samples ===