Version 0.4

Added experimental feature to merge VCF and CNR files before annotation using CNVizard's merge methods.

• Added rule in workflow/rules/cnv.smk to perform the merge of VCF and CNR files
• Added getter method for annotSV rule to handle execution paths
• Added config file option flag to activate the feature

Version 0.3

With this release, some errors in parameter handling within CNVand got fixed

• Parameter Passthrough: Fix missing passthrough of extra parameters CNVkit rules
• Model Parameter: Add a model option for the rule cnvkit_segment with separate config entry

Version 0.2

This initial (re-)release introduces CNVand, a snakemake pipeline for CNV analysis using CNVkit and AnnotSV. Key features include:

• CNV Detection: Perform target and antitarget coverage calculations, generate reference panels, correct systematic biases, segment CNVs, and classify copy number states.
• CNV Visualization: Generate detailed scatter plots in both PDF and PNG formats to visualize CNV events.
• CNV Annotation: Annotate structural variants with reference gene annotations using AnnotSV.
• Docker Support: Run the pipeline in an isolated Docker environment for consistent and reproducible results.
• Automated Reports: Generate HTML reports that include your results.