CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing
University of California, San Francisco · UCSF Helen Diller Family Comprehensive Cancer Center
Abstract
Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy…
Citation impact
- FWCI
- 86.80
- Percentile
- 100%
- References
- 47
Authors
4- ETEric Talevich
University of California, San Francisco, UCSF Helen Diller Family Comprehensive Cancer Center
- AHA. Hunter Shain
University of California, San Francisco, UCSF Helen Diller Family Comprehensive Cancer Center
- TBThomas Botton
University of California, San Francisco, UCSF Helen Diller Family Comprehensive Cancer Center
- BCBoris C. BastianCorresponding
University of California, San Francisco, UCSF Helen Diller Family Comprehensive Cancer Center
Topics & keywords
- Copy number analysis
- Copy-number variation
- Genome
- Computational biology
- Biology
- Genomics
- DNA sequencing
- Massive parallel sequencing