SVanalyzer

SVanalyzer is a software package for the analysis of large insertions, deletions, and inversions in DNA. SVanalyzer tools use repeat-aware methods to refine, compare, and cluster different structural variant calls.

Install

Using conda

SVanalyzer can be installed using the conda package manager with the bioconda channel. For details on setting up conda/bioconda, see the Bioconda user docs.

conda create -n svanalyzer
conda activate svanalyzer
conda install svanalyzer

With a release tarball/github clone

SVanalyzer can also be installed by downloading a release tarball or cloning the github repository:

git clone https://github.com/nhansen/SVanalyzer.git

After unzipping the tarball or cloning the directory, build SVanalyzer:

cd SVanalyzer
perl Build.PL
./Build
./Build test
./Build install

To install SVanalyzer to an alternate location (e.g., if you do not have root permissions), call “perl Build.PL –install_base $HOME”.

Command documentation

  • SVbenchmark - Compare a set of “test” structural variants in VCF format to a known truth set and report sensitivity and specificity
  • SVmerge - Merge similar sequence-resolved SVs in VCF format
  • SVcomp - Compare sequence-resolved SVs to each other
  • SVwiden - Add tags to a VCF file of sequence-resolved SVs detailing surrounding repetitive genomic context
  • SVrefine - Call sequence-resolved structural variants (SVs) from assembly consensus