Description
tiledbvcf is an agent skill for storing and retrieving genomic variant calls with TileDB-VCF. It is for cohort variant storage, adding samples to a store incrementally, querying by genomic interval or by sample, and exporting subsets for downstream genomics work. It ingests single-sample VCF and BCF files into an indexed store. The skill is clear about what the tool does not do. TileDB-VCF stores records. It does not perform joint variant calling, association testing, normalisation or population structure adjustment. It also warns that dataset size alone does not decide whether cloud execution is worthwhile, and recommends benchmarking the sample, region and attribute workload you actually intend to run. The skill targets the released TileDB-VCF 0.40.3. Native Python and command-line checks used two synthetic single-sample VCF files on macOS ARM64. The cloud client 0.14.4 was checked against its released wheel and mocked dispatch, and hosted queries and jobs were not executed. Use it when you have many genomes whose variant calls need to be stored and queried efficiently. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars.…
Highlights
- Indexed VCF and BCF ingestion
- Incremental cohort additions
- Interval and sample queries
- Export of subsets
- Targets TileDB-VCF 0.40.3
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tiledbvcf FAQ
What does TileDB-VCF do?
It stores and retrieves variant records from many samples, with indexed ingestion, interval and sample queries, and export.
Does it call variants?
No. The skill says it does not perform joint variant calling, association testing, normalisation or population structure adjustment.
Should I use the cloud?
The skill says dataset size alone does not decide that. Benchmark your own sample, region and attribute workload.
What was tested?
Two synthetic single-sample VCF files on macOS ARM64, and cloud contracts checked against the released wheel with mocked dispatch.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill tiledbvcf.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best tiledbvcf alternatives?
Popular alternatives to tiledbvcf include gget, biopython and bulk-rnaseq. See all tiledbvcf alternatives