Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes

Author

1. Mamunur Rashid, 
2. Carla Daniela Robles-Espinoza, 
3. Alistair G. Rust and
4. David J. Adams*

Author Affiliations

1. Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1HH

Abstract

Summary: We have developed Cake, a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. Cake can be run on a high-performance computer cluster or used as a standalone application.

Availability: Cake is open-source and is available fromhttp://cakesomatic.sourceforge.net/

Contact: [email protected]

Supplementary Information: Supplementary data are available atBioinformatics online.

• © The Author(s) 2013. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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