Viola-SV 1.0.2

SV signature analysis tool with custom SV type

Overview

Viola is a flexible and powerful python package designed specifically for analysis of genomic structural variant (SV) signatures. We provide following tools for SV signature analysis:

• Custom SV classification tool

• Feature matrix generator

• SV signature extractor (NMF) with stability evaluation system.

In addition to these, Viola offers a number of other useful utilities, including:

• VCF filter that accepts genomic coordinates and INFO/FORMAT columns.

• VCF merging tool with user-defined thresholds.

• Breakends-to-breakpoint converter with SVTYPE inference.

• Microhomology inference.

• VCF-to-BEDPE conversion.

• Command line tools for light users.

Currently, Viola supports four popular SV callers as input VCF files:

• Manta

• Delly

• Lumpy

• Gridss

In the future, we plan to support more SV callers!

Installation

The package can be installed with pip:

$ pip install viola-sv

To import Viola in your script, simply run below:

import viola

Command line tools:

$ viola <command> [something]

Prerequisites

Python version 3.6 or newer.

Recommended Environment

• OS

  • Linux

  • Mac

• Script Manager

  • Jupyter Notebook/Jupyter Lab

  • Google Colaboratory

Docker support is coming soon!

How to Learn Viola

As a first step we recommend the Quick Start page where you can see the basic behaviour of Viola. A good second step is to read the Signature Analysis Tutorial page.

For command line interfaces, see CLI tutorial.

If you want to get a deeper understanding of how Viola objects are structured, how filtering works and how merging works, please refer to the User Guide.

Manuals for individual classes/methods/functions are available in the API Reference.

For further discussion, please join our google group! We’re waiting for your comments, ideas, and requests. The questions about how to use Viola-SV are also welcome!

Documentation

• Documentation Home

• Quick Start

• Signature Analysis Tutorial

• API Reference

Publications

Sugita, I., Matsuyama, S., Dobashi, H., Komura, D. & Ishikawa, S. Viola: a structural variant signature extractor with user-defined classifications. Bioinformatics (2021) doi:10.1093/bioinformatics/btab662.