CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing.

ABSTRACT:

Background

Detecting copy number variations (CNVs) and copy number alterations (CNAs) based on whole-genome sequencing data is important for personalized genomics and treatment. CNVnator is one of the most popular tools for CNV/CNA discovery and analysis based on read depth.

Findings

Herein, we present an extension of CNVnator developed in Python-CNVpytor. CNVpytor inherits the reimplemented core engine of its predecessor and extends visualization, modularization, performance, and functionality. Additionally, CNVpytor uses B-allele frequency likelihood information from single-nucleotide polymorphisms and small indels data as additional evidence for CNVs/CNAs and as primary information for copy number-neutral losses of heterozygosity.

Conclusions

CNVpytor is significan

SUBMITTER: Suvakov M 

PROVIDER: S-EPMC8612020 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature