Just as it does for small insertions and deletions, sequence similarity at the
boundaries of large insertions and deletions can make the precise specification
of boundaries and allele sequences ambiguous.
SVanalyzer was written by Nancy Fisher Hansen, a staff scientist in the Cancer
Genetics and Comparative Genomics Branch (CGCG) of NHGRI, an institute at the
National Institutes of Health. Nancy can be reached at nhansen@mail.nih.gov.
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 https://bioconda.github.io/user/install.html.
conda create -n svanalyzer
conda activate svanalyzer
conda install -c bioconda svanalyzer- samtools v.0.1.17 or better (https://sourceforge.net/projects/samtools/files/)
Alignment tools are necessary to use the SVcomp and SVwiden commands. While
SVanalyzer will build and skip tests for these two commands if the aligners
are not installed and in the user’s path, SVanalyzer will be more functional if
these aligners are installed:
For the SVcomp, SVmerge, and SVbenchmark commands:
- edlib v.1.1.2 or better (https://github.com/Martinsos/edlib/releases)
For the SVwiden and SVrefine commands:
- MUMmer 3 (http://mummer.sourceforge.net/)
The SVbenchmark command has an option —include_bed which uses bedtools
(http://bedtools.readthedocs.io/en/latest/) to limit the structural variants
evaluated to regions specified in a BED file. The command will not run with
this option if you don’t have bedtools installed.
git clone git://github.com/nhansen/SVanalyzer.gitcd SVanalyzer
perl Build.PL
./Build
./Build test
./Build installFor local installation, call “perl Build.PL” with “—install_base $HOME”
POD documentation is contained in all modules and scripts by typing “perldoc script_or_module_name”. In
addition, detailed command options and overall usage are available at http://svanalyzer.readthedocs.io/en/latest/#.