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TileDB-VCF Genomic Variant Store

A skill for ingesting VCF/BCF variant data into TileDB sparse arrays and querying or exporting it by sample and genomic region.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 7/10Last updated: Aug 9, 2026

What it does

Guides you through the full TileDB-VCF workflow for scalable storage and retrieval of genomic variant data.

  • Installation via conda/mamba or Docker images
  • Ingesting single-sample VCFs (with .tbi/.csi indexes) and incremental sample addition without costly merges
  • Querying by region, sample list and attributes (pos_start, alleles, fmt_GT, INFO/FORMAT fields)
  • Exporting subsets to VCF/BCF/TSV; working with S3, Azure and GCS URIs
  • CLI subcommands: create, store, export, list, stat
  • Practical guidance on memory budgets, 1-based coordinates, and concurrency pitfalls
  • A checklist for scaling out to TileDB-Cloud once datasets exceed ~1000 samples

Who it's for

  • Bioinformaticians building cohort or population variant databases
  • Analysts preparing data for GWAS or rare-variant burden testing
  • Teams that continuously append new samples to a growing VCF collection
  • Engineers querying cloud-hosted variant data from pipelines

Examples

  1. "Ingest these 50 single-sample VCFs into my_dataset, then add 20 late-arriving samples" → produces incremental ingestion code that skips reprocessing.
  2. "Pull sample_name, fmt_GT, fmt_AD and fmt_DP for all samples across two chr13 regions" → builds a ds.read() query returning a pandas DataFrame.
  3. "Export only the chr21:8220186-8405573 slice for HG00097 and HG00101 as plain VCF" → drafts the ds.export() call or equivalent tiledbvcf export CLI command.

· · · Install guide · · ·

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/tiledbvcf folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/tiledbvcf/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills && mkdir -p ~/.claude/skills && cp -r /tmp/scientific-agent-skills/skills/tiledbvcf ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal (Terminal on macOS, WSL recommended on Windows).
  2. Make sure the skills directory exists: mkdir -p ~/.claude/skills
  3. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills
  4. Copy just this skill: cp -r /tmp/scientific-agent-skills/skills/tiledbvcf ~/.claude/skills/
  5. Set up the Python runtime: conda create -n tiledb-vcf "python<3.10" && conda activate tiledb-vcf, then mamba install -y -c conda-forge -c bioconda -c tiledb tiledb-py tiledbvcf-py pandas pyarrow numpy
  6. Restart Claude Code and prompt it, e.g. "use the tiledbvcf skill to ingest my VCF files".
  7. Remember: input VCFs must be single-sample and indexed (.tbi or .csi) before ingestion.
View source on GitHub ↗License: MIT