Store and query genomic variant data from VCF/BCF files using TileDB sparse arrays.
npx skills add https://github.com/mkurman/tamux --skill tiledbvcf-mkurman
Please help me install this Agent Skill. Skill: tiledbvcf Source: https://github.com/mkurman/tamux/tree/main/skills/scientific-skills/tiledbvcf Command: npx skills add https://github.com/mkurman/tamux --skill tiledbvcf-mkurman
TileDB-VCF addresses the challenge of efficiently storing, indexing, and querying large genomic variant datasets, enabling scalable ingestion and fast access to variant data across many samples and regions.
Start TileDB-VCF by initializing a dataset and ingesting your first single-sample VCF with an indexed VCF file to begin building a scalable variant database.
High-intent search queries and answers about installing and using this skill.
TileDB-VCF stores genomic variant data using sparse arrays, enabling scalable ingestion of VCF/BCF files and fast region-specific queries across thousands of samples for population genomics and cohort studies.
Yes, TileDB-VCF supports incremental sample addition, allowing you to continuously ingest single-sample VCF files with indexes into an existing variant database without reprocessing previously stored data.
TileDB-VCF performs parallel region queries across many samples, supporting INFO/FORMAT fields and cloud storage, with configurable memory budgets and region/sample partitions to ensure robust operation.
TileDB-VCF provides export capabilities to standard VCF/BCF and tabular formats, enabling reproducible pipelines and downstream analyses directly from the queried sparse array data.
Yes, TileDB-VCF supports cloud storage workflows for population genomics research and large cohort studies, offering CLI and Python interfaces to access variant data across scalable cloud environments.
Yes, TileDB-VCF requires indexed VCF files for single-sample ingestion to initialize the dataset and begin building a scalable variant database with sparse array storage.
ovachieverRead and write SAM/BAM/CRAM alignments and VCF/BCF variants using pysam.
jasrajtulsiStore and retrieve genomic variant data in TileDB-VCF format.
crazymsnStore and query large genomic variant datasets with incremental sample addition.
Lord1EgyptIngest VCF/BCF files into TileDB sparse arrays for genomic region queries.
