What problem does it solve? Working with large collections of VCF/BCF files is slow and storage-intensive, and merging multi-sample variant data for cohort studies requires expensive reprocessing every time new samples arrive. This Skill provides workflows for ingesting, querying, and exporting genomic variant data with TileDB-VCF's sparse array storage. ## Core Features & Use Cases - Incremental VCF Ingestion: Add new single-sample VCF/BCF files to an existing dataset without re-processing or merging existing data. - Parallel Region Queries: Extract variants by genomic region, sample, and attributes (GT, AD, DP, INFO/FORMAT fields) across local or cloud storage (S3, Azure, GCS). - Export and Interoperability: Export dataset subsets back to VCF/BCF or TSV for downstream tools and pipelines. - Use Case: Building a population genomics database for a GWAS cohort—ingest hundreds of single-sample VCFs, then query allele frequencies and genotypes for specific regions like chr13:32396898-32400268 across all samples in one read. ## Quick Start Create a TileDB-VCF dataset from my single-sample VCF files and query the genotypes for chromosome 1 regions across all ingested samples.
