Introduction

QuadGT workflow

QuadGT is a software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting.

Note that you can use QuadGT on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.

The software package assumes a thorough probabilistic model of single-nucleotide variants with the following notable features.

Availability

Requirements

QuadGT is implemented in 64-bit Java, and thus works on diverse platforms including Mac OS X, Microsoft Windows, and Unix/Linux flavors. The software is packaged in a JAR file (QuadGT.jar) and can be executed in Java versions 1.6 and above.

Installation

Download the JAR file QuadGT.jar. If you want to work with BAM input files, then you also need the Picard/SAMTools JDK (version 1.85). The simplest is to download QuadGT.zip which bundles QuadGT.jar with the SAMTools library. (Specifically, QuadGT.zip contains dist/QuadGT.jar and dist/lib/samtools-1.85.jar, as well as the User's Guide dist/quadgt-usage.pdf.)

Using QuadGT

User's Guide

The User's Guide is available in PDF format as quadgt-usage.pdf. It gives detailed information about command-line options, discusses the mathematical background, and provides some advice on designing variant-calling pipelines.

Plug and play

There is a built-in wizard that helps you set up then proper command-line options through a graphical interface. Execute QuadGT.jar with no arguments to launch the wizard.

% java -jar dist/QuadGT.jar & 

Acknowledgements

The QuadGT software package was developed in conjunction with a study led by Daniel Sinnett at the Sainte-Justine UHC Research Centre (Montréal, QC) on pediatric acute lymphoblastic leukemia. The project has been supported by funds from the Terry Fox Research Institute and the Canadian Institutes for Health Research, the François-Karl-Viau Research Chair in Pediatric Oncogenomics, and the National Science and Engineering Research Council.

Authors

The QuadGT software package was developed by Eric Bareke and Miklós Csűrös.

Licensing

QuadGT is distributed under the terms of a modified BSD license, as shown below

Copyright © 2012, 2013 Miklós Csűrös & Eric Bareke

All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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  3. Neither the name of the Université de Montréal nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

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