CopyDetective: Detection threshold-aware copy number variant calling in whole-exome sequencing data.

ABSTRACT:

Background

Copy number variants (CNVs) are known to play an important role in the development and progression of several diseases. However, detection of CNVs with whole-exome sequencing (WES) experiments is challenging. Usually, additional experiments have to be performed.

Findings

We developed a novel algorithm for somatic CNV calling in matched WES data called "CopyDetective". Different from other approaches, CNV calling with CopyDetective consists of a 2-step procedure: first, quality analysis is performed, determining individual detection thresholds for every sample. Second, actual CNV calling on the basis of the previously determined thresholds is performed. Our algorithm evaluates the change in variant allele frequency of polymorphisms and reports the fraction of affec

SUBMITTER: Sandmann S 

PROVIDER: S-EPMC7604644 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature