Galaxy Workflow for CNV Detection with CNVkit and Conversion to Beacon JSON Using cnv-vcf2json Version 1
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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).
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Version 1 (earliest) Created 3rd Mar 2025 at 09:03 by Khaled Jum'ah
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Created: 3rd Mar 2025 at 09:03
Last updated: 3rd Mar 2025 at 09:53
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Teams: Galaxy Training Network
Organizations: University of Bradford
Teams: Ewastools, IBISBA Workflows
Organizations: University of Bradford
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