» Articles » PMID: 27153601

Canvas: Versatile and Scalable Detection of Copy Number Variants

Overview
Journal Bioinformatics
Specialty Biology
Date 2016 May 7
PMID 27153601
Citations 110
Authors
Affiliations
Soon will be listed here.
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.

Citing Articles

Copy-number analysis from genome sequencing data of 11,754 rare-disease parent-child trios: A model for identifying autosomal recessive human gene knockouts including a novel gene for autosomal recessive retinopathy.

Olinger E, Wilson I, Orr S, Barroso-Gil M, Neatu R, Atan D Genet Med Open. 2024; 2:101834.

PMID: 39669628 PMC: 11613694. DOI: 10.1016/j.gimo.2024.101834.


Hiding in plain sight: a partial deletion of exon 7 undetectable by MLPA is a Nepali founder variant.

Clowes V, Taylor J, Pagnamenta A J Med Genet. 2024; 62(2):54-56.

PMID: 39663108 PMC: 11877027. DOI: 10.1136/jmg-2024-110422.


Molecular diagnoses and candidate gene identification in the congenital heart disease cohorts of the 100,000 genomes project.

Hartill V, Kabir M, Best S, Shaikh Qureshi W, Baross S, Lord J Eur J Hum Genet. 2024; .

PMID: 39587356 DOI: 10.1038/s41431-024-01744-2.


Identification of novel 3D-genome altering and complex structural variants underlying retinitis pigmentosa type 17 through a multistep and high-throughput approach.

de Bruijn S, Panneman D, Weisschuh N, Cadena E, Boonen E, Holtes L Front Genet. 2024; 15:1469686.

PMID: 39507620 PMC: 11537883. DOI: 10.3389/fgene.2024.1469686.


Cardiomyopathies in 100,000 genomes project: interval evaluation improves diagnostic yield and informs strategies for ongoing gene discovery.

Josephs K, Seaby E, May P, Theotokis P, Yu J, Andreou A Genome Med. 2024; 16(1):125.

PMID: 39472908 PMC: 11520845. DOI: 10.1186/s13073-024-01390-9.