Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data.

ABSTRACT:

Background

SNP arrays, short- and long-read genome sequencing are genome-wide high-throughput technologies that may be used to assay copy number variants (CNVs) in a personal genome. Each of these technologies comes with its own limitations and biases, many of which are well-known, but not all of them are thoroughly quantified.

Results

We assembled an ensemble of public datasets of published CNV calls and raw data for the well-studied Genome in a Bottle individual NA12878. This assembly represents a variety of methods and pipelines used for CNV calling from array, short- and long-read technologies. We then performed cross-technology comparisons regarding their ability to call CNVs. Different from other studies, we refrained from using the golden standard. Instead, we attempt

SUBMITTER: Lavrichenko K 

PROVIDER: S-EPMC8596897 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature