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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 |
− | 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 =>) |
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| </div> | | </div> |
| </div> | | </div> |
| + | |
| + | === 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> | | 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 = |
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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> |
| | | |
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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> |
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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> |