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tiledbvcf

Stores and queries genomic variant data in TileDB-VCF datasets using the tiledbvcf Python API and CLI (create, store, export, list, stat). Covers ingesting single-sample VCF/BCF files with .csi or .tbi indexes, adding samples incrementally, querying regions and samples in parallel, and exporting to VCF/BCF or TSV, on local disk or S3, Azure, and GCS. Use when building a variant database for a cohort, adding new samples to an existing dataset, querying specific regions across many samples, exporting subsets of a large VCF collection, or preparing population genomics data such as allele frequency or GWAS inputs. Not for multi-sample VCFs, which are unsupported, or for one-off parsing of a single VCF file.
Category: life-sciences · License: MIT · Version: 1.1

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Install

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When to use it

Stores and queries genomic variant data in TileDB-VCF datasets using the tiledbvcf Python API and CLI (create, store, export, list, stat). Covers ingesting single-sample VCF/BCF files with .csi or .tbi indexes, adding samples incrementally, querying regions and samples in parallel, and exporting to VCF/BCF or TSV, on local disk or S3, Azure, and GCS. Use when building a variant database for a cohort, adding new samples to an existing dataset, querying specific regions across many samples, exporting subsets of a large VCF collection, or preparing population genomics data such as allele frequency or GWAS inputs. Not for multi-sample VCFs, which are unsupported, or for one-off parsing of a single VCF file.

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Full playbook

Read SKILL.md for the complete workflow, references and any scripts. The agent installer copies the full skill folder.