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TileDB-VCF Genomic Variant Store

A skill for storing, ingesting, querying and exporting VCF/BCF variant data on TileDB sparse arrays for population genomics.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

  • Walks through TileDB-VCF setup (conda/mamba or Docker), dataset creation, and incremental VCF/BCF ingestion with runnable code.
  • Provides query patterns for genomic regions and sample subsets, INFO/FORMAT field extraction, and streaming of large result sets.
  • Covers export back to VCF/BCF/TSV, cloud URIs (S3, Azure, GCS), and performance tuning such as memory budget and tile cache.
  • Summarizes the CLI (create, store, export, list, stat) plus pitfalls: 1-based coordinates, single-sample VCFs only, index files required, no concurrent writers.

Who it's for

  • Population-genomics researchers repeatedly querying variants across hundreds of samples.
  • Bioinformatics engineers who need to add new samples without re-merging existing cohorts.
  • Teams building GWAS or rare-variant burden testing data pipelines.

Examples

  1. "Ingest these 50 single-sample VCFs into a TileDB dataset" → checks index prerequisites and emits ingest_samples code.
  2. "Pull GT and DP for every sample in chr13:32396898-32397044" → generates the matching ds.read(...) call.
  3. "Export only chr21 for two samples as VCF" → produces ds.export(...) or the equivalent tiledbvcf export CLI command.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/tiledbvcf/SKILL.md

What I want: (describe your task here)

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↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

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/sci-skills && mkdir -p ~/.claude/skills && cp -r /tmp/sci-skills/skills/tiledbvcf ~/.claude/skills/

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

  1. Open a terminal.
  2. Clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Create the skills folder: mkdir -p ~/.claude/skills
  4. Copy this skill: cp -r scientific-agent-skills/skills/tiledbvcf ~/.claude/skills/
  5. Restart Claude Code and ask "do you have the tiledbvcf skill?" to confirm it loaded.
  6. Prepare the runtime: conda create -n tiledb-vcf "python<3.10", then mamba install -c conda-forge -c bioconda -c tiledb tiledb-py tiledbvcf-py.
  7. Verify your VCFs are single-sample and indexed (.tbi or .csi) before ingesting.
View source on GitHub ↗License: MIT