Galaxy Workflow for CNV Detection with CNVkit and Conversion to Beacon JSON Using cnv-vcf2json Version 1
Download RO-Crate
Run on GalaxyThis Galaxy workflow streamlines comprehensive copy number variation (CNV) analysis by integrating CNVkit’s robust detection capabilities with an efficient conversion step using cnv-vcf2json to format results into Beacon JSON. Designed for computational biologists and bioinformaticians, the workflow standardizes CNV identification and output formatting to enhance interoperability with Beacon networks. It is specifically optimized for use with mapped BAM files from the EGAD00001008392 synthetic dataset, leveraging spiked-in variant data from RD-Connect GPAP synthetic data (available at Zenodo).
Version History
Version 1 (earliest) Created 3rd Mar 2025 at 09:03 by Khaled Jum'ah
Initial commit
Open
master7c74287
Creators and SubmitterViews: 119 Downloads: 25 Runs: 1
Created: 3rd Mar 2025 at 09:03
Last updated: 3rd Mar 2025 at 09:53
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: University of Bradford
Teams: Ewastools, IBISBA Workflows
Organizations: University of Bradford
https://orcid.org/0000-0001-6173-5674
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
