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VIPER (Variant InsPector and Expert Rating tool) can be utilised to view variant calls and decide whether or not those are true or false positives.
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README.md

VIPER (Variant InsPector and Expert Rating tool) can be utilised to view variant calls and decide whether or not those are true or false positives. All calls are visualised using IGV, thus enabling fast rating of sv calls. VIPER is implemented using Java and AngularJS.

If you are using VIPER for the first time, you should have a look at at the short tutorial.

Requirements

To run the VIPER server, Java version 1.8 is required. You can check your java version by running java -version in a console. Make sure to use a modern web browser, as VIPER is heavily reliant on the browser's Javascript environment.

Installation

It is advised to use the VIPER and IGV jar files (as well as example configuration files) that can be downloaded from the GitHub release pages. If you are using Linux, it is recommended to install Xvfb with sudo apt-get install xvfb You can then run VIPER with java -jar VIPER.jar config.json to start the VIPER server, and open http://localhost:8090 in a browser tab.

To build VIPER from source, bower and gradle need to be installed. You can then use ./build.sh to create an executable version of the VIPER server.

Configuration

VIPER can be configured using a .json file. There are mandatory and optional parameters that change the way VIPER operates.

Required parameters

These parameters act as input to the VIPER server and must be specified by the user:

parameter description
analysisFile File containing variant calls (must be a .csv or .vcf file). .csv files must include a header with column names. Columns sample, type, chr1, bp1, chr2 and bp2 are mandatory.
workDir Directory that stores images by igv and decision progress. WARNING: Do not delete this directory, or your progress will be lost
bamDir Directory containing your .bam/.bai sample files.

Optional parameters

These parameters are optional and may be omitted using the default values:

parameter description default value
enableGrouping Group together calls with same chromosome values and similar breakpoint values true
breakpointTolerance If grouping is enabled, this is the maximum distance where two breakpoints are considered similar. 3
csvDelimiter Character that delimits csv columns. ";"
collectionDelimiter A single cell in a csv table may have multiple values. These values are seperated by this character. ","
partnerFile CSV file containing partnering information (i.e., control-tumor pairs, trios). When used, VIPER offers to inspect the partner samples as well as the sample the respective variant was called in. null
partnerDelimiter Delimiter used when reading partnering information. ","
viperPort Port that VIPER listens on. 8090
igvPort Port that IGV uses to communicate with VIPER 9090
fastaRef .fasta reference file or IGV reference key (e.g. hg19). Set to a .fasta file for improved performance. "hg19"
numPrecomputedSnapshots Precompute this number of breakpoint images to minimize visualization waiting time. 10
keepVcfSimple Use only mandatory vcf columns and ignore additional INFO and genotype information false
excludeRefVcfCalls Ignore calls that are marked as reference calls. true
igvJar Path to IGV jar file. "igv.jar"
xvfbDisplay When using Xvfb, use this number as display number. 1234
xvfbWidth When using Xvfb, create a window with this width. 1280
xvfbHeight When using Xvfb, create a window with this height. 1680
igvMaxMemory Maximum heap size of the IGV process. 1200
xslxExportWindowSize When creating .xlsx files, this improves memory usage. Only change if exceptions occur during .xlsx export. 1000
igvLog File containing IGV logs igv.log
sleepInterval Time to wait between IGV commands 0

Examples

Some example .bam files and sample .csvcall files can be found on Sciebo.

Improving VIPER

You encountered any errors or have ideas that might improve VIPER? Feel free to open an issue or write me an e-mail: mar.w@wwu.de

Citing

Please make sure to cite the applications note when using VIPER for research purposes:

Marius Wöste, Martin Dugas; VIPER: a web application for rapid expert review of variant calls, Bioinformatics


The VIPER icon was provided by courtesy of Niké Jenny Bruinsma.

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