Copy Number Variants

Sergii Ivakhno, Eric Roller, Ivakhno, Sergii, Roller, Eric

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, polyclonality in cancer samples, or frequency of de novo variation in germline genomes of pedigrees. The frequent need of core sequencing facilities to process samples from both normal and tumor sources favors multipurpose variant calling tools with functionality to process these diverse sets within a single software framework. This not only simplifies the overall bioinformatics workflow but also streamlines maintenance by shortening the software update cycle and requiring only limited staff training. Here we introduce Canvas, a tool for identification of copy number changes from diverse sequencing experiments including whole-genome matched tumor-normal, small pedigree, and single-sample normal resequencing, 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.