M3vcftools - Revision history

Santy.8128: /* Download */

2016-07-11T01:57:19Z

Download

← Older revision		Revision as of 21:57, 10 July 2016
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	\|-		\|-
	\| m3vcftools Source Files		\| m3vcftools Source Files
	\| [ftp://share.sph.umich.edu/~~m3vcftools~~/m3vcftools.v1.0.1.tar.gz UNIX Users ]		\| [ftp://share.sph.umich.edu/minimac3/m3vcftools.v1.0.1.tar.gz UNIX Users ]

	\|}		\|}

Santy.8128: /* Usage */

2015-10-18T04:38:40Z

Usage

← Older revision		Revision as of 00:38, 18 October 2015
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	For e.g. to calculate LD the command should be: <code>../bin/m3vcftools --vcf INPUT.m3vcf.gz --hap-r2 --ld-window-bp 10000 --min-r2 0.4 --out PREFIX</code>		For e.g. to calculate LD the command should be: <code>../bin/m3vcftools --vcf INPUT.m3vcf.gz --hap-r2 --ld-window-bp 10000 --min-r2 0.4 --out PREFIX</code>

	For e.g. to convert a VCF file into M3VCF format : <code>../bin/m3vcftools --vcf INPUT.vcf.gz --recode --out PREFIX</code>		For e.g. to convert a VCF file into M3VCF format : <code>../bin/m3vcftools --vcf INPUT.vcf.gz --recode --out PREFIX</code>


	= 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].

Santy.8128 at 04:38, 18 October 2015

2015-10-18T04:38:29Z

← Older revision		Revision as of 00:38, 18 October 2015
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	= Usage=		= Usage=

	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 '''m3vcftools ''' (if they downloaded the source files).

	## EXTRACT ~~MINIMAC3~~ AND COMPILE		## EXTRACT M3VCFTOOLS AND COMPILE

	tar -xzvf ~~Minimac3~~.v1.0.13.tar.gz		tar -xzvf m3vcftools.v1.0.1.tar.gz
	cd ~~Minimac3~~/		cd m3vcftools /
	make		make

			For e.g. to calculate LD the command should be: <code>../bin/m3vcftools --vcf INPUT.m3vcf.gz --hap-r2 --ld-window-bp 10000 --min-r2 0.4 --out PREFIX</code>
			For e.g. to convert a VCF file into M3VCF format : <code>../bin/m3vcftools --vcf INPUT.vcf.gz --recode --out PREFIX</code>


	= 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].

Santy.8128 at 04:37, 18 October 2015

2015-10-18T04:37:15Z

@@ Line 54: / Line 54: @@
   cd Minimac3/
   make
 = Contact =
 In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].

Santy.8128: /* Download */

2015-10-18T04:36:32Z

Download

← Older revision		Revision as of 00:36, 18 October 2015
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	'''m3vcftools''' is currently available as a pilot version. Please see our wiki page on [[M3vcftools Usage \| m3vcftools Usage Options]] for more details on available options.		'''m3vcftools''' is currently available as a pilot version. Please see our wiki page on [[M3vcftools Usage \| m3vcftools Usage Options]] for more details on available options.

	The software is in a very developmental mode and new options are going to be added regularly. '''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/m3vcftools-help&umich.edu mailing list]''' to get updates about future releases or provide us with feedback about possible bug reports, remarks on documentation, '''or new feature requests that you might want early'''. User could also email ~~them~~ to [mailto:sayantan@umich.edu Sayantan Das].		The software is in a very developmental mode and new options are going to be added regularly. '''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/m3vcftools-help&umich.edu mailing list]''' to get updates about future releases or provide us with feedback about possible bug reports, remarks on documentation, '''or new feature requests that you might want early'''. User could also email their queries/feedback to [mailto:sayantan@umich.edu Sayantan Das].

			'''VERSION: 1.0.1 !!! (Updated 10.25.2015) !!!'''

			'''Github Repo:''' Users can clone from github repository as well : [https://github.com/Santy-8128/m3vcftools m3vcftools Github]
	~~'''VERSION: 1.0.13 !!! (Updated 10.15.2015) !!!'''~~

	'''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 !!!'''		'''Cloning from GitHub is recommened so that updates can be easily pulled back !!!'''
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	! Download Link		! Download Link
	\|-		\|-
	\| ~~Minimac3~~ Source Files		\| m3vcftools Source Files
	\| [ftp://share.sph.umich.edu/~~minimac3~~/~~Minimac3~~.v1.0.13.tar.gz UNIX Users ]		\| [ftp://share.sph.umich.edu/m3vcftools/m3vcftools.v1.0.1.tar.gz UNIX Users ]

	\|}		\|}

Santy.8128: /* Download */

2015-10-18T04:35:09Z

Download

← Older revision		Revision as of 00:35, 18 October 2015
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	'''m3vcftools''' is currently available as a pilot version. Please see our wiki page on [[M3vcftools Usage \| m3vcftools Usage Options]] for more details on available options.		'''m3vcftools''' is currently available as a pilot version. Please see our wiki page on [[M3vcftools Usage \| m3vcftools Usage Options]] for more details on available options.

	The software is in a very developmental mode and new options are going to be added regularly. '''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/m3vcftools-help&umich.edu\|mailing list]''' to get updates about future releases or provide us with feedback about possible bug reports, remarks on documentation, '''or new feature requests that you might want early'''. User could also email them to [mailto:sayantan@umich.edu Sayantan Das].		The software is in a very developmental mode and new options are going to be added regularly. '''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/m3vcftools-help&umich.edu mailing list]''' to get updates about future releases or provide us with feedback about possible bug reports, remarks on documentation, '''or new feature requests that you might want early'''. User could also email them to [mailto:sayantan@umich.edu Sayantan Das].

Santy.8128 at 04:34, 18 October 2015

2015-10-18T04:34:43Z

← Older revision		Revision as of 00:34, 18 October 2015
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	= Useful Wiki Pages =		= Useful Wiki Pages =

	There are a few pages in this Wiki that may be useful to for '''~~Minimac3~~''' users. Here are links to a few:		There are a few pages in this Wiki that may be useful to for '''m3vcftools''' users. Here are links to a few:

	* [[M3vcftools\| m3vcftools Overview Page]]		* [[M3vcftools\| m3vcftools Overview Page]]

	* [[M3vcftools Usage \| m3vcftools Usage ~~and Documentation~~]]		* [[M3vcftools Usage \| m3vcftools Usage Options]]

	* [[M3vcftools Examples\| m3vcftools Examples]]		* [[M3vcftools Examples\| m3vcftools Examples]]
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	= Download =		= Download =

	'''~~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~~]].		'''m3vcftools''' is currently available as a pilot version. Please see our wiki page on [[M3vcftools Usage \| m3vcftools Usage Options]] for more details on available options.

			The software is in a very developmental mode and new options are going to be added regularly. '''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/m3vcftools-help&umich.edu\|mailing list]''' to get updates about future releases or provide us with feedback about possible bug reports, remarks on documentation, '''or new feature requests that you might want early'''. User could also email them to [mailto:sayantan@umich.edu Sayantan Das].


	'''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/minimac3-help&umich.edu\| mailing list] to get updates about future releases or report possible bugs or email them to [mailto:sayantan@umich.edu Sayantan Das].'''

	'''VERSION: 1.0.13 !!! (Updated 10.15.2015) !!!'''		'''VERSION: 1.0.13 !!! (Updated 10.15.2015) !!!'''

Santy.8128: /* Introduction */

2015-10-18T02:37:30Z

Introduction

← Older revision		Revision as of 22:37, 17 October 2015
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	= Introduction =		= Introduction =

	'''m3vcftools''' is a tool (exactly similar to '''vcftools''') but will be much faster and can be used for simple data query and basic summary like allele frequency, linkage-r2 calculation, etc. '''m3vcftools''' is ideal for mega reference panels like '''Haplotye Reference Consortium (HRC)''' with over 32,000 samples where '''m3vcftools is 70-90 times faster than vcftools (18 mins vs 28 hours)''' in calculating AF or LD summaries. For panels like '''1000 Genomes Phase 3, m3vcftools is 12-15 times faster'''.		'''m3vcftools''' is a tool (exactly similar to [http://vcftools.sourceforge.net/ '''vcftools''']) but will be much faster and can be used for simple data query and basic summary like allele frequency, linkage-r2 calculation, etc. '''m3vcftools''' is ideal for mega reference panels like [http://www.haplotype-reference-consortium.org/ '''Haplotye Reference Consortium (HRC)'''] with over 32,000 samples where '''m3vcftools is 70-90 times faster than vcftools (18 mins vs 28 hours)''' in calculating AF or LD summaries. For panels like '''[[Minimac3#Reference Panels for Download \| 1000 Genomes Phase 3]], m3vcftools is 12-15 times faster'''.

	The command line format for m3vcftools is going to be exactly same as that of vcftools, thus users wouldn't have to learn a new tool or change their already existing pipelines. The only difference would lie in the fact that m3vcftools usually takes M3VCF files has input instead of VCF files. Of course, the tool itself can convert a VCF file into M3VCf format which can then later be used for fast data query and summary statistics calculations.		The command line format for m3vcftools is going to be exactly same as that of vcftools, thus users wouldn't have to learn a new tool or change their already existing pipelines. The only difference would lie in the fact that m3vcftools usually takes M3VCF files has input instead of VCF files. Of course, the tool itself can convert a VCF file into M3VCf format which can then later be used for fast data query and summary statistics calculations.

Santy.8128: /* Introduction */

2015-10-18T02:34:37Z

Introduction

← Older revision		Revision as of 22:34, 17 October 2015
Line 18:		Line 18:

	= Introduction =		= Introduction =

	'''Minimac3 ''' is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in [[Minimac\|minimac]] and [[Minimac2\|minimac2]]. '''Minimac3''' is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. It accomplishes this by identifying repeat haplotype patterns and using these to simplify the underlying calculations, with no loss of accuracy.

	Minimac3 uses [[M3VCF Files\|<font face=Courier>M3VCF</font> files]] (customized minimac3 VCF files) to store reference panel information in a compact form, thus saving on memory and time required to read large datasets. Users can use Minimac3 to convert standard VCF files to <font face=Courier>M3VCF</font> files. <font face=Courier>M3VCF</font> files can also store pre-calculated estimates of recombination fraction and error, which speeds up later rounds of imputation. Minimac3 outputs results in the form of standard VCF files for easy data manipulation in downstream analysis.

	'''m3vcftools''' is a tool (exactly similar to '''vcftools''') but will be much faster and can be used for simple data query and basic summary like allele frequency, linkage-r2 calculation, etc. '''m3vcftools''' is ideal for mega reference panels like '''Haplotye Reference Consortium (HRC)''' with over 32,000 samples where '''m3vcftools is 70-90 times faster than vcftools (18 mins vs 28 hours)''' in calculating AF or LD summaries. For panels like '''1000 Genomes Phase 3, m3vcftools is 12-15 times faster'''.		'''m3vcftools''' is a tool (exactly similar to '''vcftools''') but will be much faster and can be used for simple data query and basic summary like allele frequency, linkage-r2 calculation, etc. '''m3vcftools''' is ideal for mega reference panels like '''Haplotye Reference Consortium (HRC)''' with over 32,000 samples where '''m3vcftools is 70-90 times faster than vcftools (18 mins vs 28 hours)''' in calculating AF or LD summaries. For panels like '''1000 Genomes Phase 3, m3vcftools is 12-15 times faster'''.

Santy.8128: /* Introduction */

2015-10-18T02:34:10Z

Introduction

← Older revision		Revision as of 22:34, 17 October 2015
Line 22:		Line 22:

	Minimac3 uses [[M3VCF Files\|<font face=Courier>M3VCF</font> files]] (customized minimac3 VCF files) to store reference panel information in a compact form, thus saving on memory and time required to read large datasets. Users can use Minimac3 to convert standard VCF files to <font face=Courier>M3VCF</font> files. <font face=Courier>M3VCF</font> files can also store pre-calculated estimates of recombination fraction and error, which speeds up later rounds of imputation. Minimac3 outputs results in the form of standard VCF files for easy data manipulation in downstream analysis.		Minimac3 uses [[M3VCF Files\|<font face=Courier>M3VCF</font> files]] (customized minimac3 VCF files) to store reference panel information in a compact form, thus saving on memory and time required to read large datasets. Users can use Minimac3 to convert standard VCF files to <font face=Courier>M3VCF</font> files. <font face=Courier>M3VCF</font> files can also store pre-calculated estimates of recombination fraction and error, which speeds up later rounds of imputation. Minimac3 outputs results in the form of standard VCF files for easy data manipulation in downstream analysis.

			'''m3vcftools''' is a tool (exactly similar to '''vcftools''') but will be much faster and can be used for simple data query and basic summary like allele frequency, linkage-r2 calculation, etc. '''m3vcftools''' is ideal for mega reference panels like '''Haplotye Reference Consortium (HRC)''' with over 32,000 samples where '''m3vcftools is 70-90 times faster than vcftools (18 mins vs 28 hours)''' in calculating AF or LD summaries. For panels like '''1000 Genomes Phase 3, m3vcftools is 12-15 times faster'''.

			The command line format for m3vcftools is going to be exactly same as that of vcftools, thus users wouldn't have to learn a new tool or change their already existing pipelines. The only difference would lie in the fact that m3vcftools usually takes M3VCF files has input instead of VCF files. Of course, the tool itself can convert a VCF file into M3VCf format which can then later be used for fast data query and summary statistics calculations.

	= Download =		= Download =