A read visualizer for structural variants
Project description
Author: Noah Spies
svviz visualizes high-throughput sequencing data relevant to a structural variant. Only reads supporting the variant or the reference allele will be shown. svviz can operate in both an interactive web browser view to closely inspect individual variants, or in batch mode, allowing multiple variants (annotated in a VCF file) to be analyzed simultaneously.
See the documentation for more detailed help, or run svviz -h to get help on command line arguments.
Quickstart
Ensure that you have a working compiler by following these instructions (OS X only) and that the python package pip is installed.
Install the latest version of svviz from github using the following terminal command: sudo pip install -U svviz. (The sudo may not be necessary depending on your setup.)
Run the following command, which downloads example data and runs it through svviz: svviz demo. After several processing steps, a web browser window should open, with separate, interactive views of the reference and alternate alleles.
Please report any issues using the github issue tracker.
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