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.


Software dependencies

SVanalyzer tools require samtools (, the edlib aligner (, MUMmer (, and bedtools ( to perform its structural variant comparisons.

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

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

cd SVanalyzer
perl Build.PL
./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