CANVAS

Description

canvas website

Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data. It can work either with germline data, or paired tumor/normal samples. Its primary input is aligned reads (in .bam format), and its primary output is a report (in a .vcf file) giving the copy number status of the genome.

Environment Modules

Run module spider canvas to find out what environment modules are available for this application.

Environment Variables

• HPC_CANVAS_DIR - installation directory
• HPC_CANVAS_BIN - executable directory

Citation

If you publish research that uses canvas you have to cite it as follows:

Roller, E., Ivakhno, S., Lee, S., Royce, T., & Tanner, S. (2016). Canvas: Versatile and scalable detection of copy number variants. Bioinformatics, 32(15), 2375–2377. https://doi.org/10.1093/bioinformatics/btw163

Pedersen, B. S., Layer, R. M., & Quinlan, A. R. (2017). Canvas SPW: Calling de novo copy number variants in pedigrees. Bioinformatics, 33(15), 2437–2443. https://doi.org/10.1093/bioinformatics/btx618

Categories

phylogenetics