CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.

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 number evenly across the genome. This combination achieves both exon-level resolution

SUBMITTER: Talevich E 

PROVIDER: S-EPMC4839673 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature