Feature Request: Add Option to Generate Subset BAMs for Screenshots and Variant Confirmation

[berntpopp]

Description

Add an option to the script to generate subset BAM files for screenshots and variant confirmation. This feature should ideally remove traceable information such as read names and BAM headers to maintain privacy and security.

Proposed Changes

1. Add Option for Subset BAM Generation:

   • Introduce a new command-line option to enable the generation of subset BAM files.
   • Example: --generate-subset-bam true/false (default: false)

2. Remove Traceable Information:

   • Ensure that traceable information such as read names and BAM headers are removed from the subset BAM files.

3. Implement Subset BAM Generation:

   • Implement the functionality to generate subset BAM files that contain only the reads of interest.
   • Ensure that the BAM files generated are suitable for use in screenshots and variant confirmation.

4. Update Documentation:

   • Update the script documentation to include details about the new option and how to use it.

Steps to Implement

1. Modify the script to accept the new --generate-subset-bam option.
2. Implement functionality to generate subset BAM files.
3. Remove traceable information from the subset BAM files.
4. Test the implementation to ensure it works correctly.
5. Update the documentation with usage instructions and examples.

Impact

This enhancement will provide users with a convenient way to generate subset BAM files for screenshots and variant confirmation while ensuring that traceable information is removed for privacy and security.

Additional Notes

• Ensure backward compatibility with the current script functionality.
• Provide clear usage instructions and examples in the updated documentation.

[berntpopp]

Likely easier with igv-reports