ArticleGigaScience2021
CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing.
Article in GigaScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed.
- Whole genome sequencing of 1427 Mexican individuals from the oriGen cohort.Nature communications · 2026Article
- BioTester: an AI-driven automated testing framework for identifying potential quality risks in bioinformatics software.Briefings in bioinformatics · 2026Article
- Functional noncoding variants within the TBX1 enhancer contribute to tetralogy of Fallot.Science China. Life sciences · 2026Article
- Whole genome copy number variation analysis to detect genomic regions for resistance to Haemonchus contortus in Sheep.BMC genomics · 2026Article
- Multiple modes of selection underlie repeated and human-mediated adaptation in a formerly migratory fish.Molecular biology and evolution · 2026Article
- Genetic Heterogeneity of Autism Spectrum Disorder: Identification of Five Novel Mutations (RIMS2, FOXG1, AUTS2, ZCCHC17, and SPTBN5) in Iranian Families via Whole-Exome and Whole-Genome Sequencing.Biochemical genetics · 2026Article
- Maternal copy number variations detected by noninvasive prenatal testing in Japanese women.Journal of human genetics · 2026Article
- Short-read genome sequencing at population scale: diagnostic insights from 2317 patients.European journal of human genetics : EJHG · 2026Article
- Crucial parameters for precise copy number variation detection in formalin-fixed paraffin-embedded solid cancer samples.Molecular oncology · 2026Article
- Functional impact of genetic background on variable expressivity in neurodevelopmental disorders.Nature communications · 2026Article
- Parallel analysis of replication timing, gene expression, and copy number with PARTAGE.Genome research · 2026Article
- WeavePop: a bioinformatics workflow to explore and analyze genomic variants of eukaryotic populations.G3 (Bethesda, Md.) · 2026Article
- Genome-Wide Analysis of Copy Number Variation in Vietnamese Local Chickens.Animals : an open access journal from MDPI · 2026Article
- High-resolution Chromosomal Microarray with Diagnostic Potential for Detecting Exon-level Copy Number Variations Using Targeted and Non-targeted Approaches.Annals of laboratory medicine · 2026Article
- Pivotal role of biallelic frequency analysis in identifying copy number alterations using genome-wide methods in tumors with a high level of aneuploidy.Journal of applied genetics · 2026Article
- Persistence and spread of fluconazole-resistantMicrobial genomics · 2026Article
- Long-read genome sequencing enhances diagnostics of pediatric neurological disorders.Genome medicine · 2026Article
- Detection and evaluation of copy number variation using both linked-read and short-read sequencing in New Zealand dairy cattle.Frontiers in genetics · 2026Article
- An integrated platform for concurrent structural and single-nucleotide variants improves copy-number detection and reveals pathogenic alleles in undiagnosed Mendelian families.Genome medicine · 2025Article
- Multi-omics analysis delineates molecular signatures of spinal ependymal tumor.Cellular oncology (Dordrecht, Netherlands) · 2025Article
26 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
backgroundDetecting 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.
findingsHerein, 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.
conclusionsCNVpytor is significantly faster than CNVnator-particularly for parsing alignment files (2-20 times faster)-and has (20-50 times) smaller intermediate files. CNV calls can be filtered using several criteria, annotated, and merged over multiple samples. Modular architecture allows it to be used in shared and cloud environments such as Google Colab and Jupyter notebook. Data can be exported into JBrowse, while a lightweight plugin version of CNVpytor for JBrowse enables nearly instant and GUI-assisted analysis of CNVs by any user. CNVpytor release and the source code are available on GitHub at https://github.com/abyzovlab/CNVpytor under the MIT license.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.