Related Issues (20)
- Check Input files format in replace GT script
- long options handling not implemented for all in filter_phenotypes.sh
- Feature request: Configurable delimiters in filter_variants.sh
- Add version information of other tools to logging
- Add links to documentation, repository and help email
- Feature request: add check if the Gene name was found
- Feature request: add counts for individuals with a specific variant HOT 1
- Feature request: add option to perform gene burden analysis HOT 2
- Documentation: add installation instruction
- Refactor: main script in main folder and helpers in subfolders
- Documentaion: Filter Logic and Available Annotations
- Enhancement: Add Interactive CLI Prompts
- Enhancement: Add Option to Filter by Position or Specific Variants HOT 1
- Documentation: Update README and Usage Description with Examples for All Scripts
- Documentation: Add Detailed Examples for All Scripts
- Feature Request: Add Script to Generate IGV Browser Screenshots HOT 1
- Documentation: Add Installation Instructions for All Required Tools
- Feature request: Use Phenopackets for HPO filtering input
- Feature request: Conda env as parameter
- Feature request: Investigate multiple VCFs as input HOT 1
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