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Canvas: versatile and scalable detection of copy number variants

Eric Roller, Sergii Ivakhno, Steve Lee, Thomas Royce, Stephen Tanner
doi: https://doi.org/10.1101/036194
Eric Roller
1Illumina Inc., 5200 Illumina Way, San Diego, CA 92122
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Sergii Ivakhno
2Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL
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Steve Lee
1Illumina Inc., 5200 Illumina Way, San Diego, CA 92122
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Thomas Royce
3Ashion Analytics, 445 North 5th Street, Phoenix, AZ
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Stephen Tanner
1Illumina Inc., 5200 Illumina Way, San Diego, CA 92122
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Abstract

Motivation: Increased throughput and diverse experimental designs of large-scale sequencing studies necessi-tate versatile, scalable and robust variant calling tools. In particular, identification of copy number changes re-mains 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 se-quencing 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 simple to execute workflows that can scale to thousands of samples and can be easily incorporated into existing variant calling pipelines.

Availability: Canvas is distributed under an open source license and can be downloaded from https://github.com/Illumina/canvas.

Contact: eroller{at}illumina.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 13, 2016.
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Canvas: versatile and scalable detection of copy number variants
Eric Roller, Sergii Ivakhno, Steve Lee, Thomas Royce, Stephen Tanner
bioRxiv 036194; doi: https://doi.org/10.1101/036194
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Canvas: versatile and scalable detection of copy number variants
Eric Roller, Sergii Ivakhno, Steve Lee, Thomas Royce, Stephen Tanner
bioRxiv 036194; doi: https://doi.org/10.1101/036194

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