Vt - Revision history

Atks: /* General */

2021-05-04T08:36:58Z

General

← Older revision		Revision as of 04:36, 4 May 2021
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	2. cd vt <br>		2. cd vt <br>
	#update submodules		#update submodules
	3.git submodule update --init --recursive <br>		3. git submodule update --init --recursive <br>
	#run make, note that compilers need to support the c++0x standard		#run make, note that compilers need to support the c++0x standard
	4. make <br>		4. make <br>

2021-05-04T08:36:21Z

General

← Older revision		Revision as of 04:36, 4 May 2021
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	2. cd vt <br>		2. cd vt <br>
	#update submodules		#update submodules
	3.git submodule update --init --recursive		3.git submodule update --init --recursive <br>
	#run make, note that compilers need to support the c++0x standard		#run make, note that compilers need to support the c++0x standard
	4. make <br>		4. make <br>

2021-05-04T08:35:05Z

General

← Older revision		Revision as of 04:35, 4 May 2021
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	#change directory to vt		#change directory to vt
	2. cd vt <br>		2. cd vt <br>
			#update submodules
			3.git submodule update --init --recursive
	#run make, note that compilers need to support the c++0x standard		#run make, note that compilers need to support the c++0x standard
	3. make <br>		4. make <br>
	#you can test the build		#you can test the build
	4. make test		5. make test
	<div class=" mw-collapsible mw-collapsed">		<div class=" mw-collapsible mw-collapsed">
	An expected output when all is well for the tests is shown here. (click expand =>)		An expected output when all is well for the tests is shown here. (click expand =>)

2020-06-10T00:09:34Z

Remove overlap

← Older revision		Revision as of 20:09, 9 June 2020
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	</div>		</div>

	=== ~~Remove~~ overlap ===		=== Filter overlap ===

	Removes overlapping variants in a VCF file by tagging such variants with the FILTER flag overlap.		Removes overlapping variants in a VCF file by tagging such variants with the FILTER flag overlap.

	<div class=" mw-collapsible mw-collapsed">		<div class="mw-collapsible mw-collapsed">
	#annotates variants that are overlapping		#annotates variants that are overlapping
	vt ~~remove_overlap~~ in.vcf -r hs37d5.fa -o overlapped.tagged..vcf		vt filter_overlap in.vcf -r hs37d5.fa -o overlapped.tagged..vcf

	<div class="mw-collapsible-content">		<div class="mw-collapsible-content">
	usage : vt ~~remove_overlap~~ [options] <in.vcf>		usage : vt filter_overlap [options] <in.vcf>

	options : -o output VCF file [-]		options : -o output VCF file [-]
			-w window overlap for variants [0]
	-I file containing list of intervals []		-I file containing list of intervals []
	-i intervals []		-i intervals []
	-? displays help		-? displays help
			</div>
			</div>

			<div class="mw-collapsible mw-collapsed">
			#Use Remove overlap instead for versions older than Jan 12, 2017
			vt remove_overlap in.vcf -r hs37d5.fa -o overlapped.tagged..vcf

			<div class="mw-collapsible-content">
			usage: vt remove_overlap [options] <in.vcf>
			The old version has the same options except that it lacks the -w option
			The change occurred in the following commit:
			https://github.com/atks/vt/commit/ab5cf7e91b3baa5349f439e6fe92491ae19da1a6
	</div>		</div>
	</div>		</div>

2019-10-23T11:24:52Z

Decompose biallelic block substitutions

← Older revision		Revision as of 07:24, 23 October 2019
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	description : decomposes biallelic block substitutions into its constituent SNPs. <br>		description : decomposes biallelic block substitutions into its constituent SNPs. <br>
	usage : vt decompose_blocksub [options] <in.vcf> <br>		usage : vt decompose_blocksub [options] <in.vcf> <br>
	options : -a enable aggressive/alignment mode		options : -m keep MNVs (multi-nucleotide variants) [false]
			-a enable aggressive/alignment mode [false]
			-d MNVs max distance (when -m option is used) [2]
	-o output VCF file [-]		-o output VCF file [-]
	-I file containing list of intervals []		-I file containing list of intervals []
	-i intervals []		-i intervals []
	-? displays help		-? displays help-a enable aggressive/alignment mode

	</div>		</div>
	</div>		</div>

2019-10-23T11:19:28Z

Decompose biallelic block substitutions

← Older revision		Revision as of 07:19, 23 October 2019
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	There is now an additional option -a which decomposes non block substitutions into its constituent SNPs and indels. (kindly added by [[https://github.com/holtgrewe holtgrewe@github]]) <br>		There is now an additional option -a which decomposes non block substitutions into its constituent SNPs and indels. (kindly added by [[https://github.com/holtgrewe holtgrewe@github]]) <br>
	There is no exact solution and this decomposition is based on the best guess outcome using a Needleman-Wunsch algorithm. <br>		There is no exact solution and this decomposition is based on the best guess outcome using a Needleman-Wunsch algorithm. <br>
	You might also want to check out [https://github.com/vcflib/vcflib#vcfallelicprimitives vcfallelicprimitives].		You might also want to check out [https://github.com/vcflib/vcflib#vcfallelicprimitives vcfallelicprimitives]. <br>
			<br>
			There is now an additional option -m and -d which ensures that some MNVs are not decomposed. (kindly added by [[https://github.com/jaudoux jaudoux@github]]) <br>
			The motivation is from<br>
			*Exome-wide assessment of the functional impact and pathogenicity of multi-nucleotide mutations https://www.biorxiv.org/content/10.1101/258723v2.full<br>
			*Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes https://www.biorxiv.org/content/10.1101/573378v2.full<br>
	</div>		</div>

2018-07-25T01:48:47Z

Mac

← Older revision		Revision as of 21:48, 24 July 2018
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	=== Mac ===		=== Mac ===

			You may install vt via homebrew.

	brew tap brewsci/bio		brew tap brewsci/bio

2018-07-25T01:48:10Z

Mac

← Older revision		Revision as of 21:48, 24 July 2018
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	=== Mac ===		=== Mac ===

	~~You will need to install the package xz prior to installing vt.~~		brew tap brewsci/bio
			brew tap brewsci/science
	~~homebrew~~ install xz
			brew install brewsci/bio/vt

2018-03-02T05:03:02Z

Mac

← Older revision		Revision as of 01:03, 2 March 2018
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	Building has been tested on Linux and Mac systems on gcc 4.8.1 and clang 3.4. <br>		Building has been tested on Linux and Mac systems on gcc 4.8.1 and clang 3.4. <br>
	Some features of C++11 is used, thus there is a need for newer versions of gcc and clang.		Some features of C++11 are used, thus there is a need for newer versions of gcc and clang.

	= Updating =		= Updating =

2018-03-01T19:35:30Z

Installation

← Older revision		Revision as of 15:35, 1 March 2018
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	</div>		</div>
	</div>		</div>

			=== Mac ===

			You will need to install the package xz prior to installing vt.

			homebrew install xz


	Building has been tested on Linux and Mac systems on gcc 4.8.1 and clang 3.4. <br>		Building has been tested on Linux and Mac systems on gcc 4.8.1 and clang 3.4. <br>