Canvas: versatile and scalable detection of copy number variants
Open Access
- 24 March 2016
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 32 (15), 2375-2377
- https://doi.org/10.1093/bioinformatics/btw163
Abstract
Motivation: Versatile and efficient variant calling tools are needed to analyze large scale sequencing datasets. In particular, identification of copy number changes remains a challenging task due to their complexity, susceptibility to sequencing biases, variation in coverage data and dependence on genome-wide sample properties, such as tumor polyploidy or polyclonality in cancer samples. Results: We have developed a new tool, Canvas, for identification of copy number changes from diverse sequencing experiments including whole-genome matched tumor-normal and single-sample normal re-sequencing, as well as whole-exome matched and unmatched tumor-normal studies. In addition to variant calling, Canvas infers genome-wide parameters such as cancer ploidy, purity and heterogeneity. It provides fast and easy-to-run workflows that can scale to thousands of samples and can be easily incorporated into variant calling pipelines. Availability and Implementation: Canvas is distributed under an open source license and can be downloaded from https://github.com/Illumina/canvas. Contact:eroller@illumina.com Supplementary information: Supplementary data are available at Bioinformatics online.Keywords
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