tiledbvcf
Category: life-sciences · License: MIT · Version: 1.1
Tags: genomic variants, VCF, variant storage, population genomics
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.Example requests
Ask your agent in plain language, for example:- “How do I add 20 new samples to an existing TileDB-VCF dataset without redoing the old ones?”
- “I’ve got 400 single-sample gVCFs from our mouse cohort in s3://lab-mouse/vcfs/ (each with a .tbi). I ran
tiledbvcf storeinto s3://lab-mouse/db and it died with an out-of-memory error partway through. How should I set it up so I can resume and then pull chr2:1000000-2000000 for 50 named samples into a TSV with sample, pos, ref, alt, and genotype?” - “We’re preparing inputs for a GWAS and a rare-variant burden test. Our sequencing center delivers one VCF per individual, about 600 people, and every analysis starts by pulling the same few hundred candidate gene regions across everyone. Re-scanning the files each time is painfully slow. What’s a better way to organize this data?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.