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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 <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>
#you can test the build
#you can test the build
5. make test
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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 =>)
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=== Mac ===
You may install vt via homebrew.
brew tap brewsci/bio
brew tap brewsci/science
brew install brewsci/bio/vt
Building has been tested on Linux and Mac systems on gcc 4.8.1 and clang 3.4. <br>
Some features of C++11 are used, thus there is a need for newer versions of gcc and clang.
= Updating =
= Updating =
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>
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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
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#converts in.bcf to tab format with selected INFO fields
#converts in.bcf to tab format with selected INFO and FILTER fields
vt info2tab in.bcf -v -t EX_RL,FZ_RL,MDUST,LOBSTR,VNTRSEEK,RMSK,EX_REPEAT_TRACT
vt info2tab in.bcf -u PASS -t EX_RL,FZ_RL,MDUST,LOBSTR,VNTRSEEK,RMSK,EX_REPEAT_TRACT
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INPUT
INPUT
OUTPUT
OUTPUT
======
======
CHROM POS REF ALT N_ALLELE EX_RL FZ_RL MDUST LOBSTR VNTRSEEK RMSK EX_REPEAT_TRACT_1 EX_REPEAT_TRACT_2
CHROM POS REF ALT N_ALLELE PASS EX_RL FZ_RL MDUST LOBSTR VNTRSEEK RMSK EX_REPEAT_TRACT_1 EX_REPEAT_TRACT_2
20 17548608 A AC 2 2 13 1 1 0 0 17548608 17548608
20 17548608 A AC 2 1 2 13 1 1 0 0 17548608 17548608
20 17548608 AAAAG A 2 4 13 1 1 0 0 17548609 17548609
20 17548608 AAAAG A 2 1 4 13 1 1 0 0 17548609 17548609
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usage : vt info2tab [options] <in.vcf>
usage : vt info2tab [options] <in.vcf>
options : -v print variant CHROM,POS,REF,ALT,N_ALLELE [false]
options : -d debug [false]
-f filter expression []
-f filter expression []
-t list of info tags to be extracted []
-u list of filter tags to be extracted []-t list of info tags to be extracted []
-o output tab delimited file [-]
-o output tab delimited file [-]
-I file containing list of intervals []
-I file containing list of intervals []
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=== 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.
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#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
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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
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#Use Remove overlap instead for versions older than Jan 12, 2017
vt remove_overlap in.vcf -r hs37d5.fa -o overlapped.tagged..vcf
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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
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