1,102
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→General
#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
<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 =>)
</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>
