- Delete references/population_genomics.md
- Remove all references to deleted documentation files
- Clean up References section since no reference files remain
- Simplify skill to standalone main file only
- Delete detailed export and ingestion reference documentation
- Update main skill to remove references to deleted files
- Simplify skill to focus on core querying and population genomics
- Keep querying.md and population_genomics.md reference files
- All documentation is at https://cloud.tiledb.com/academy/
- Remove incorrect service URLs (docs.tiledb.com, support portal, etc.)
- Consolidate to academy and main platform URLs only
- Update contact information to sales@tiledb.com
- Replace incorrect subcommands (create-dataset, ingest, list-datasets)
- Use correct subcommands: create, store, export, list, stat, utils, version
- Update examples to match actual CLI usage patterns
- Add comprehensive list of all available subcommands with descriptions
- VCFs must be single-sample (multi-sample not supported)
- Index files (.csi or .tbi) are required for all VCF/BCF files
- Add indexing examples with bcftools and tabix
- Document requirements prominently in both main skill and ingestion guide
- Correct method: tiledb.cloud.vcf.read() not query_variants()
- Fix parameter: attrs not attributes
- Add namespace parameter for billing account
- Add .to_pandas() conversion step
- Use realistic example with TileDB-Inc dataset URI
- Remove Java references (focus on Python and CLI)
- Move all TileDB-Cloud content to bottom of document
- Update export example to show VCF format with .export() method
- Simplify 'When to Use' section focusing on open source capabilities
- Better document organization with cloud scaling at the end
- Add preferred conda environment setup with Python <3.10
- Include M1 Mac specific configuration (CONDA_SUBDIR=osx-64)
- Install tiledbvcf-py via mamba from tiledb channel
- Restore normal Python examples (not Docker-only)
- Keep Docker as alternative installation method
- Correct installation method: Docker images, not pip packages
- Update examples to show Docker container usage
- Based on actual TileDB-VCF repository documentation
- Add comprehensive TileDB-VCF skill by Jeremy Leipzig
- Covers open source TileDB-VCF for learning and moderate-scale work
- Emphasizes TileDB-Cloud for large-scale production genomics (1000+ samples)
- Includes detailed reference documentation:
* ingestion.md - Dataset creation and VCF ingestion
* querying.md - Efficient variant queries
* export.md - Data export and format conversion
* population_genomics.md - GWAS and population analysis workflows
- Features accurate TileDB-Cloud API patterns from official repository
- Highlights scale transition: open source → TileDB-Cloud for enterprise
