Minimac3 Examples - Revision history

Santy.8128: /* Examples */

2015-09-11T06:15:20Z

Examples

← Older revision		Revision as of 02:15, 11 September 2015
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	--doseOutput		--doseOutput

	For examples on imputation of chromosome X, see [[#Minimac3 Cookbook : Chromosome X Imputation\|Chromosome X Imputation]]		For examples on imputation of chromosome X, see [[Minimac3 Cookbook : Chromosome X Imputation\|Chromosome X Imputation]]

	= Download =		= Download =

Santy.8128: /* Examples */

2015-09-11T06:14:46Z

Examples

← Older revision		Revision as of 02:14, 11 September 2015
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	--doseOutput		--doseOutput

	For examples on imputation of chromosome X, see [[#Chromosome X Imputation\|Chromosome X Imputation]]		For examples on imputation of chromosome X, see [[#Minimac3 Cookbook : Chromosome X Imputation\|Chromosome X Imputation]]

	= Download =		= Download =

Santy.8128: /* Useful Wiki Pages */

2015-01-30T03:28:35Z

Useful Wiki Pages

← Older revision		Revision as of 23:28, 29 January 2015
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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 Examples\| Minimac3 Examples]]		* [[Minimac3 Examples\| Minimac3 Examples]]

Santy.8128: /* Download */

2015-01-30T00:34:40Z

Download

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 '''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]].
 = Contact =
 In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].

Santy.8128: /* Download */

2015-01-30T00:15:32Z

Download

@@ Line 69: / Line 69: @@
 = Download =
-'''Minimac3 ''' is available as an undocumented release version. The source files are available for download here and commonly used reference panels in <code>M3VCF</code> format are available for download in [[#Reference Panels for Download | Reference Panels]].
+'''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]].
 = Contact =
 In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].

Santy.8128: /* Examples */

2015-01-29T05:05:33Z

Examples

← Older revision		Revision as of 01:05, 29 January 2015
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	= Examples =		= Examples =

	Here we give some examples of using Minimac3 for typical imputation experiments. Users should check the wiki pages on [[Minimac3 Usage\|Minimac3 Usage]] and [[Minimac3 Imputation Cookbook \| Imputation Cookbook]] ~~and~~ for further details on available parameter options.		Here we give some examples of using Minimac3 for typical imputation experiments. Users should also check the wiki pages on [[Minimac3 Usage\|Minimac3 Usage]] and [[Minimac3 Imputation Cookbook \| Imputation Cookbook]] for further details on available parameter options and imputing GWAS samples.

	All example data sets used below are available in the '''Minimac3''' package available for download [[#Download\|here]]. Users should follow the following steps to compile '''Minimac3''' (after downloading it) and then move to directory Minimac3/test/ before running the examples given below.		All example data sets used below are available in the '''Minimac3''' package available for download [[#Download\|here]]. Users should follow the following steps to compile '''Minimac3''' (after downloading it) and then move to directory Minimac3/test/ before running the examples given below.

Santy.8128: /* Examples */

2015-01-29T05:04:54Z

Examples

← Older revision		Revision as of 01:04, 29 January 2015
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	= Examples =		= Examples =

	Here we give some examples of using Minimac3 for typical imputation experiments. Users should check the wiki pages on [[Minimac3 Usage\|Minimac3 Usage]] and [[Minimac3 Imputation Cookbook \| Imputation Cookbook]]and for further details on available parameter options.		Here we give some examples of using Minimac3 for typical imputation experiments. Users should check the wiki pages on [[Minimac3 Usage\|Minimac3 Usage]] and [[Minimac3 Imputation Cookbook \| Imputation Cookbook]] and for further details on available parameter options.

	All example data sets used below are available in the '''Minimac3''' package available for download [[#Download\|here]]. Users should follow the following steps to compile '''Minimac3''' (after downloading it) and then move to directory Minimac3/test/ before running the examples given below.		All example data sets used below are available in the '''Minimac3''' package available for download [[#Download\|here]]. Users should follow the following steps to compile '''Minimac3''' (after downloading it) and then move to directory Minimac3/test/ before running the examples given below.

Santy.8128: /* Examples */

2015-01-29T05:04:38Z

Examples

← Older revision		Revision as of 01:04, 29 January 2015
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	= Examples =		= Examples =

	Here we give some examples of using Minimac3 for typical imputation experiments. Users should check the wiki ~~page~~ on [[Minimac3 Usage\|Minimac3 Usage]] for further details on available parameter options.		Here we give some examples of using Minimac3 for typical imputation experiments. Users should check the wiki pages on [[Minimac3 Usage\|Minimac3 Usage]] and [[Minimac3 Imputation Cookbook \| Imputation Cookbook]]and for further details on available parameter options.

	All example data sets used below are available in the '''Minimac3''' package available for download [[#Download\|here]]. Users should follow the following steps to compile '''Minimac3''' (after downloading it) and then move to directory Minimac3/test/ before running the examples given below.		All example data sets used below are available in the '''Minimac3''' package available for download [[#Download\|here]]. Users should follow the following steps to compile '''Minimac3''' (after downloading it) and then move to directory Minimac3/test/ before running the examples given below.

Santy.8128: /* Examples */

2015-01-29T05:02:45Z

Examples

← Older revision		Revision as of 01:02, 29 January 2015
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	= Examples =		= Examples =

	Here we give some examples of using Minimac3 for typical imputation experiments. Users should check wiki page on [[Minimac3 Usage\|Minimac3 Usage]] for further details on available parameter options.		Here we give some examples of using Minimac3 for typical imputation experiments. Users should check the wiki page on [[Minimac3 Usage\|Minimac3 Usage]] for further details on available parameter options.

	All example data sets used below are available in the '''Minimac3''' package available for download [[#Download\|here]]. Users should follow the following steps to compile '''Minimac3''' after downloading it.		All example data sets used below are available in the '''Minimac3''' package available for download [[#Download\|here]]. Users should follow the following steps to compile '''Minimac3''' (after downloading it) and then move to directory Minimac3/test/ before running the examples given below.

	## EXTRACT MINIMAC3 AND COMPILE		## EXTRACT MINIMAC3 AND COMPILE

Santy.8128: /* Examples */

2015-01-29T05:01:33Z

Examples

← Older revision		Revision as of 01:01, 29 January 2015
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	= Examples =		= Examples =

	~~To look at the~~ examples~~, the folder~~ of ~~'''~~Minimac3 ~~''' needs to be copied to the users local directory first~~. ~~Then move to the folder <font face=Courier>LocalDirectory/test/</font>~~		Here we give some examples of using Minimac3 for typical imputation experiments. Users should check wiki page on [[Minimac3 Usage\|Minimac3 Usage]] for further details on available parameter options.

	cp -~~r /net/fantasia/home/sayantan/Softwares/~~Minimac3/ ~~LocalDirectoryMinimac3/~~		All example data sets used below are available in the '''Minimac3''' package available for download [[#Download\|here]]. Users should follow the following steps to compile '''Minimac3''' after downloading it.
	cd ~~LocalDirectoryMinimac3/~~test/
			## EXTRACT MINIMAC3 AND COMPILE

			tar -xzvf Minimac3.v1.0.0.tar.gz
			cd Minimac3/
			make
			cd test/

	The following example uses a VCF reference file <font face=Courier>[refPanel.vcf]</font> and a VCF target sample file <font face=Courier>[targetStudy.vcf]</font>		The following example uses a VCF reference file <font face=Courier>[refPanel.vcf]</font> and a VCF target sample file <font face=Courier>[targetStudy.vcf]</font>