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 ### Does NOT Trigger | Scenario | Use Instead | |----------|-------------| | Reading, filtering, or iterating a handful of VCF/BAM files in Python (pysam/htslib) | `alterlab-pysam` | | Producing the VCFs in the first place (FASTQ -> alignment -> variant calling) | `alterlab-nf-core-sarek` | | Clinical interpretation or population frequency of a specific variant | `alterlab-clinvar` / `alterlab-gnomad` | | General chunked array storage for non-variant data (images, tensors, matrices) | `alterlab-zarr` | | Out-of-c...