title: Canvas: versatile and scalable detection of copy number variants.
abstract: 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.
  
  
  
  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.
  
  
  
  Canvas is distributed under an open source license and can be downloaded from https://github.com/Illumina/canvas
  
  
  
  eroller@illumina.com
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Illumina Inc, San Diego, CA 92122, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Roller
authors.affiliation: Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
authors.forename: Sergii
authors.initials: S
authors.lastname: Ivakhno
authors.affiliation: Illumina Inc, San Diego, CA 92122, USA.
authors.forename: Steve
authors.initials: S
authors.lastname: Lee
authors.affiliation: Ashion Analytics, Phoenix, AZ, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Royce
authors.affiliation: Illumina Inc, San Diego, CA 92122, USA.
authors.forename: Stephen
authors.initials: S
authors.lastname: Tanner
mesh_terms: D000465:Algorithms; D056915:DNA Copy Number Variations; D059472:Exome; D006801:Humans; D009369:Neoplasms; D012984:Software