Ingest VCF/BCF files into TileDB sparse arrays for genomic variant queries.
npx skills add https://github.com/shushuzn/Rairos --skill tiledbvcf-shushuzn
Please help me install this Agent Skill. Skill: tiledbvcf Source: https://github.com/shushuzn/Rairos/tree/main/skills/tiledbvcf Command: npx skills add https://github.com/shushuzn/Rairos --skill tiledbvcf-shushuzn
This skill solves the problem of storing and querying large genomic variant datasets efficiently while avoiding slow, costly re-merging and enabling fast region- and sample-scoped access.
Use case examples:
Use the tiledbvcf skill to create a TileDB-VCF dataset and ingest indexed single-sample VCFs so you can query specific regions across chosen samples.
High-intent search queries and answers about installing and using this skill.
To query genomic variants fast, ingest single-sample VCF/BCF files into a TileDB sparse array. This enables high-performance region- and sample-scoped reads without expensive dataset re-merging.
Yes, you can add new samples to an existing TileDB-VCF dataset incrementally. This supports cohort growth over time by allowing population genomics samples to be ingested as they arrive without costly rebuilding.
You can export VCF subsets by performing parallel querying across chosen genomic intervals and samples. The extracted variant attributes are generated as standard VCF or TSV outputs for downstream analysis pipelines.
Yes, single-sample VCF or BCF inputs require accompanying index files to ingest genomic data into a TileDB sparse array. Inputs use 1-based VCF coordinate semantics for accurate variant positioning.
Yes, TileDB-VCF supports scalable local or cloud dataset access across S3, Azure, and GCS. This enables querying and exporting genomic variant data directly from cloud storage platforms.
Yezez9Ingest VCF/BCF files into TileDB arrays for scalable genomic variant queries.
ovachieverRead and write SAM/BAM/CRAM alignments and VCF/BCF variants using pysam.
Lord1EgyptIngest VCF/BCF files into TileDB sparse arrays for genomic region queries.
tassiovaleManage genomic variant data with TileDB-VCF for scalable storage and querying.
