alterlab-tiledbvcf

# TileDB-VCF ## Overview TileDB-VCF is a high-performance C++ library with Python and CLI interfaces for efficient storage and retrieval of genomic variant-call data. Built on TileDB's sparse array technology, it enables scalable ingestion of VCF/BCF files, incremental sample addition without expensive merging operations, and efficient parallel queries of variant data stored locally or in the cloud. ## When to Use This Skill This skill should be used when: - Building a queryable, compressed variant store from many single-sample VCF/BCF files (cohort/population datasets too large for flat VCF) - Incrementally adding new samples to an existing store without re-merging - Querying specific genomic regions across many samples (region/sample-partitioned reads) - Exporting region/sample subsets back to VCF/BCF for downstream tools - Working with variant data on cloud storage (S3, Azure, GCS) or TileDB Cloud - Prototyping or teaching scalable genomics-variant workflows ## Quick Start ### Installation **Preferred method: conda/mamba from the `tiledb` channel.** `tiledbvcf-py` is NOT on PyPI, conda-forge, or bioconda — it ships from the `tiledb` Anaconda channel, with native `osx-arm64` builds (no Rosetta/`CONDA_SUBDIR` workaround needed on Apple Silicon). Supports Python 3.9–3.12. ```bash # Native Apple Silicon (osx-arm64) — also works on osx-64 / linux-64 conda create -n tiledb-vcf -c conda-forge -c tiledb \ python=3.12 tiledbvcf-py=0.40 pandas pyarrow numpy conda activate t...