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Bioinformatics. 2016 Aug 1;32(15):2375-7. doi: 10.1093/bioinformatics/btw163. Epub 2016 Mar 24.

Canvas: versatile and scalable detection of copy number variants.

Author information

1
Illumina Inc, San Diego, CA 92122, USA.
2
Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
3
Ashion Analytics, Phoenix, AZ, USA.

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.

PMID:
27153601
DOI:
10.1093/bioinformatics/btw163
[Indexed for MEDLINE]

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