svviz
A read visualizer to validate structural variants
Quick Start
- From the terminal, install the latest version of svviz from pypi:
sudo pip install -U svviz - Run the following command:
svviz demo
See the documentation for more detailed installation instructions.
Overview
Features
svviz visualizes high-throughput sequencing data supporting a structural variant
-
Reconstructs alternate allele sequence
Reads are aligned against the reconstructed alternate allele sequence – no more awkward visual contortions of the standard reference genome.
-
Supports any read data in BAM format
Supports short reads, for example from Illumina short-fragment and mate-pair libraries
Also supports long read data, such as Moleculo (assembled), MinIon or PacBio.
-
Realignment around breakpoints
Performs a full Smith-Waterman alignment so that reads are aligned across structural variant breakpoints.
-
Interactive browser view
Supports zooming in and out and shows detailed information about each read upon request.
-
Export to PNG, PDF or SVG
Export to vector or raster image formats from the browser view or directly from the command-line.
-
Batch mode
Analyze many putative structural variants simultaneously from an input VCF file.
Long reads
Example heterozygous insertion fully spanned by multiple PacBio reads.
The insertion is shown in blue, replacing a short deleted segment colored orange.
Multiple samples
Example deletion in a trio; based on svviz's output, mother and son appear to be heterozygous for the deletion, while the father is homozygous (only a single read supports the reference, with minimal overlap with the deletion).
Interactive browser interface
Get detailed information about individual reads, SNP positions and more in the browser interface.
More information
svviz was developed by Noah Spies with support from the National Institute of Standards and Technology and the Sidow lab at Stanford University.