diff --git a/scientific-skills/tiledbvcf/SKILL.md b/scientific-skills/tiledbvcf/SKILL.md index 8391795..cd5e97e 100644 --- a/scientific-skills/tiledbvcf/SKILL.md +++ b/scientific-skills/tiledbvcf/SKILL.md @@ -269,28 +269,34 @@ ds = tiledbvcf.Dataset(uri="gcs://bucket/dataset", mode="r") ## CLI Usage -TileDB-VCF provides a powerful command-line interface: +TileDB-VCF provides a command-line interface with the following subcommands: + +**Available Subcommands:** +- `create` - Creates an empty TileDB-VCF dataset +- `store` - Ingests samples into a TileDB-VCF dataset +- `export` - Exports data from a TileDB-VCF dataset +- `list` - Lists all sample names present in a TileDB-VCF dataset +- `stat` - Prints high-level statistics about a TileDB-VCF dataset +- `utils` - Utils for working with a TileDB-VCF dataset +- `version` - Print the version information and exit ```bash -# Create and ingest data -tiledbvcf create-dataset --uri my_dataset -tiledbvcf ingest --uri my_dataset sample1.vcf.gz sample2.vcf.gz +# Create empty dataset +tiledbvcf create --uri my_dataset -# Query and export +# Ingest samples (requires single-sample VCFs with indexes) +tiledbvcf store --uri my_dataset --samples sample1.vcf.gz,sample2.vcf.gz + +# Export data tiledbvcf export --uri my_dataset \ --regions "chr1:1000000-2000000" \ - --sample-names "sample1,sample2" \ - --output-format bcf \ - --output-path output.bcf + --sample-names "sample1,sample2" -# List dataset info -tiledbvcf list-datasets --uri my_dataset +# List all samples +tiledbvcf list --uri my_dataset -# Export as TSV -tiledbvcf export --uri my_dataset \ - --regions "chr1:1000000-2000000" \ - --tsv-fields "CHR,POS,REF,ALT,S:GT" \ - --output-format tsv +# Show dataset statistics +tiledbvcf stat --uri my_dataset ``` ## Advanced Features