SVanalyzer

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h1. SVanalyzer modules/scripts

p. 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.

p. 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 [email protected].

h2. Software dependencies

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.

h2. Installing with conda

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.

bc.. conda create -n svanalyzer conda activate svanalyzer conda install -c bioconda svanalyzer

h2. Building github version on your own: Dependencies

• 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.

h2. Building github version on your own: Instructions

h3. Clone the repository

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

h3. Build SVanalyzer

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

h3. Local installation

p. For local installation, call "perl Build.PL" with "--install_base $HOME"

h2. Documentation

p. 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/#.