Overview
In this release, we developed a tool to readily grab allele frequency data: the Cohort Allele Frequency Generator (CAF generator)! Briefly, we designed a project plugin architecture, which makes it easier to query AnVIL data projects on a variant level. Using example plugins for both open access (1000 Genomes) and restricted access (GREGoR) Workspaces, you can create a project plugin once and reuse it many times! Plus, our starter notebook, example plugins, and utility methods make it easier to understand how to get started.
Through our work, we hope to reduce the barriers to querying user-specified AnVIL cohorts while increasing the standardization of allelic data into [GA4GH formats](https://va-ga4gh.readthedocs.io/en/1.0.0-ballot.2024-11/base-profiles/study-result-profiles.html#cohort-allele-frequency-study-result).
Other than the plugin infrastructure, some speed-ups and ease-of-use changes were made to the `vrs_bulk annotate` CLI tool, which allows you to readily find matches of raw VCF variants to downstream knowledge bases like MetaKB.
Getting Started
Installation
sh
pip install vrs-anvil-toolkit
Terra!
For those familiar with Terra, you can find the workspace hosting all of our tooling, setup, and additional workflows on our Terra [VRS AnVIL Workspace](https://app.terra.bio/#workspaces/terra-test-bwalsh/vrs_anvil).
CAF Generation
For creating CAFs and designing plugins, see our README for more info on how to [get started](https://github.com/gks-anvil/vrs_anvil_toolkit#cohort-allele-frequency-generation).
What's Changed
* Small VCF Annotation: First Pass w/out Terra Testing by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/4
* Initial Scaling of VCF to Evidence Processing by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/12
* Add 1000G test for small vcf by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/17
* Feature/gnomad formatting by bwalsh in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/18
* Adds disk cache by bwalsh in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/19
* Feature/packaging by bwalsh in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/20
* Fix/cache dir by bwalsh in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/27
* Feature/gather scatter gather by bwalsh in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/34
* bugs/terra-testing by bwalsh in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/41
* Improve README by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/32
* Feature/metakb by bwalsh in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/43
* chore/fix-coding-conventions by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/53
* Update VRS-Python to 2.0.05a by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/55
* Feature/metakb-results by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/56
* Cleanup/bugs and tests by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/57
* Feature/example scripts by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/62
* feature/better-threaded-translator by bwalsh in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/63
* Feature/figure improvements by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/67
* renames cmd to vrs_bulk by bwalsh in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/76
* Usage docs by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/87
* feature/terra-setup by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/90
* save manifest to file by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/85
* feature/making-cache-scalable by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/89
* bump version 0.1.0 by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/91
* TKEDTE-309 Explore GREGOR VCF->Participant->Phenotype by bwalsh in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/93
* update uris to gks-anvil org by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/99
* [TKEDTE-341] Feature/plugin-initial-refactor by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/102
* Feature/standardized output rebase by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/109
**Full Changelog**: https://github.com/gks-anvil/vrs_anvil_toolkit/commits/0.2.0rc5
* Update README.md Logo by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/110
* v0.3.0: Building Cohort Allele Frequency objects with Plugins! by quinnwai in https://github.com/gks-anvil/vrs_anvil_toolkit/pull/111
**Full Changelog**: https://github.com/gks-anvil/vrs_anvil_toolkit/compare/0.2.0rc5...0.3.0