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.
SVanalyzer tools require samtools (http://www.htslib.org), the edlib aligner (https://github.com/Martinsos/edlib), MUMmer (https://github.com/mummer4/mummer), and bedtools (http://bedtools.readthedocs.io/en/latest/) to perform its structural variant comparisons.
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¶
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”.
- 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