Genome-wide analysis and visualization of copy number with CNVpytor in igv.js.
Bioinformatics
; 40(8)2024 08 02.
Article
em En
| MEDLINE
| ID: mdl-39018173
ABSTRACT
SUMMARY:
Copy number variation (CNV) and alteration (CNA) analysis is a crucial component in many genomic studies and its applications span from basic research to clinic diagnostics and personalized medicine. CNVpytor is a tool featuring a read depth-based caller and combined read depth and B-allele frequency (BAF) based 2D caller to find CNVs and CNAs. The tool stores processed intermediate data and CNV/CNA calls in a compact HDF5 file-pytor file. Here, we describe a new track in igv.js that utilizes pytor and whole genome variant files as input for on-the-fly read depth and BAF visualization, CNV/CNA calling and analysis. Embedding into HTML pages and Jupiter Notebooks enables convenient remote data access and visualization simplifying interpretation and analysis of omics data. AVAILABILITY AND IMPLEMENTATION The CNVpytor track is integrated with igv.js and available at https//github.com/igvteam/igv.js. The documentation is available at https//github.com/igvteam/igv.js/wiki/cnvpytor. Usage can be tested in the IGV-Web app at https//igv.org/app and also on https//github.com/abyzovlab/CNVpytor.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Software
/
Genômica
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Variações do Número de Cópias de DNA
Limite:
Humans
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article