# DivBase

> A service to manage, query and version VCF files and associated sample metadata.

DivBase is a platform for centralized storage, collaborative sharing, and queryable access to genomic VCF variant files and associated sample metadata.
Users interact with DivBase via `divbase-cli` (CLI) or the web interface at https://divbase.scilifelab-2-prod.sys.kth.se.
Queries combine bcftools-based VCF filtering with sidecar TSV sample metadata filtering.

- [llms-users.txt](https://scilifelabdatacentre.github.io/divbase/llms-users.txt): User guides and CLI reference concatenated in a single file (~200 KB)
- [llms-full.txt](https://scilifelabdatacentre.github.io/divbase/llms-full.txt): Complete documentation, including the developer guide, concatenated in a single file (~400 KB)

## DivBase

- [DivBase](https://scilifelabdatacentre.github.io/divbase/)

## User Guides

- [Overview](https://scilifelabdatacentre.github.io/divbase/user-guides/)
- [Quick Start Guide](https://scilifelabdatacentre.github.io/divbase/user-guides/quick-start/)
- [FAQ](https://scilifelabdatacentre.github.io/divbase/user-guides/faq/)
- [Account Management](https://scilifelabdatacentre.github.io/divbase/user-guides/account-management/)
- [Installation](https://scilifelabdatacentre.github.io/divbase/user-guides/installation/)
- [Setup DivBase CLI](https://scilifelabdatacentre.github.io/divbase/user-guides/setup_divbase_cli/)
- [Managing Project Files](https://scilifelabdatacentre.github.io/divbase/user-guides/files/)
- [Working with VCF Files in DivBase](https://scilifelabdatacentre.github.io/divbase/user-guides/vcf-files/)
- [Overview](https://scilifelabdatacentre.github.io/divbase/user-guides/running-queries-overview/)
- [VCF Dimensions caching](https://scilifelabdatacentre.github.io/divbase/user-guides/vcf-dimensions/)
- [Sidecar Metadata TSV files: creating and querying sample metadata files](https://scilifelabdatacentre.github.io/divbase/user-guides/sidecar-metadata/)
- [VCF query syntax](https://scilifelabdatacentre.github.io/divbase/user-guides/vcf-query-syntax/)
- [How to create efficient DivBase queries](https://scilifelabdatacentre.github.io/divbase/user-guides/how-to-create-efficient-divbase-queries/)
- [Tutorial: Running a query on a public dataset](https://scilifelabdatacentre.github.io/divbase/user-guides/tutorial-query-on-public-data/)
- [Managing Project Versions](https://scilifelabdatacentre.github.io/divbase/user-guides/project-versioning/)
- [Using DivBase Programmatically](https://scilifelabdatacentre.github.io/divbase/user-guides/using-divbase-programmatically/)
- [Troubleshooting](https://scilifelabdatacentre.github.io/divbase/user-guides/troubleshooting/)

## CLI Commands

- [Overview](https://scilifelabdatacentre.github.io/divbase/cli/)
- [divbase-cli](https://scilifelabdatacentre.github.io/divbase/cli/_auto_generated/divbase-cli/)
- [divbase-cli config](https://scilifelabdatacentre.github.io/divbase/cli/_auto_generated/config/)
- [divbase-cli auth](https://scilifelabdatacentre.github.io/divbase/cli/_auto_generated/auth/)
- [divbase-cli files](https://scilifelabdatacentre.github.io/divbase/cli/_auto_generated/files/)
- [divbase-cli query](https://scilifelabdatacentre.github.io/divbase/cli/_auto_generated/query/)
- [divbase-cli version](https://scilifelabdatacentre.github.io/divbase/cli/_auto_generated/version/)
- [divbase-cli dimensions](https://scilifelabdatacentre.github.io/divbase/cli/_auto_generated/dimensions/)
- [divbase-cli task-history](https://scilifelabdatacentre.github.io/divbase/cli/_auto_generated/task-history/)

## Dev Guide

- [Overview](https://scilifelabdatacentre.github.io/divbase/development/)
- [Setup Guide](https://scilifelabdatacentre.github.io/divbase/development/setup/)
- [API](https://scilifelabdatacentre.github.io/divbase/development/api/)
- [Bcftools Celery Task Logic](https://scilifelabdatacentre.github.io/divbase/development/bcftools_task_logic/)
- [Bcftools Celery Task Constraints](https://scilifelabdatacentre.github.io/divbase/development/bcftools_task_constraints/)
- [Benchmarking Scripts](https://scilifelabdatacentre.github.io/divbase/development/benchmarking_scripts/)
- [Deployment](https://scilifelabdatacentre.github.io/divbase/development/deployment/)
- [Celery Task Implementation](https://scilifelabdatacentre.github.io/divbase/development/celery_task_implementation/)
- [Contributing to DivBase development](https://scilifelabdatacentre.github.io/divbase/CONTRIBUTING/)
- [Database Migrations](https://scilifelabdatacentre.github.io/divbase/development/database-migrations/)
- [Documentation](https://scilifelabdatacentre.github.io/divbase/development/documentation/)
- [Key design decisions related to VCF files](https://scilifelabdatacentre.github.io/divbase/development/key_design_decisions_related_to_vcf_files/)
- [Logging](https://scilifelabdatacentre.github.io/divbase/development/logging/)
- [Monitoring and observability](https://scilifelabdatacentre.github.io/divbase/development/monitoring_and_observability/)
- [Monitoring Celery Worker Metrics](https://scilifelabdatacentre.github.io/divbase/development/worker_metrics/)
- [Personal Access Tokens](https://scilifelabdatacentre.github.io/divbase/development/personal_access_tokens/)
- [Sending Emails](https://scilifelabdatacentre.github.io/divbase/development/sending-emails/)
- [Security Policy](https://scilifelabdatacentre.github.io/divbase/SECURITY/)
- [Sidecar sample metadata TSV queries](https://scilifelabdatacentre.github.io/divbase/development/metadata_queries/)
- [S3 Transfers](https://scilifelabdatacentre.github.io/divbase/development/s3_transfers/)
- [Task History Implementation](https://scilifelabdatacentre.github.io/divbase/development/task_history_implementation/)
- [Testing](https://scilifelabdatacentre.github.io/divbase/development/testing/)
- [Writing E2E Tests for VCF Results Checksums](https://scilifelabdatacentre.github.io/divbase/development/writing_e2e_tests_for_vcf_results_checksums/)

## Releases

- [Releases](https://scilifelabdatacentre.github.io/divbase/releases/)