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.
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
pip install vrs-anvil-toolkitTerra!
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.
CAF Generation
For creating CAFs and designing plugins, see our README for more info on how to get started.
What's Changed
- Small VCF Annotation: First Pass w/out Terra Testing by @quinnwai in #4
- Initial Scaling of VCF to Evidence Processing by @quinnwai in #12
- Add 1000G test for small vcf by @quinnwai in #17
- Feature/gnomad formatting by @bwalsh in #18
- Adds disk cache by @bwalsh in #19
- Feature/packaging by @bwalsh in #20
- Fix/cache dir by @bwalsh in #27
- Feature/gather scatter gather by @bwalsh in #34
- bugs/terra-testing by @bwalsh in #41
- Improve README by @quinnwai in #32
- Feature/metakb by @bwalsh in #43
- chore/fix-coding-conventions by @quinnwai in #53
- Update VRS-Python to 2.0.05a by @quinnwai in #55
- Feature/metakb-results by @quinnwai in #56
- Cleanup/bugs and tests by @quinnwai in #57
- Feature/example scripts by @quinnwai in #62
- feature/better-threaded-translator by @bwalsh in #63
- Feature/figure improvements by @quinnwai in #67
- renames cmd to vrs_bulk by @bwalsh in #76
- Usage docs by @quinnwai in #87
- feature/terra-setup by @quinnwai in #90
- save manifest to file by @quinnwai in #85
- feature/making-cache-scalable by @quinnwai in #89
- bump version 0.1.0 by @quinnwai in #91
- TKEDTE-309 Explore GREGOR VCF->Participant->Phenotype by @bwalsh in #93
- update uris to gks-anvil org by @quinnwai in #99
- [TKEDTE-341] Feature/plugin-initial-refactor by @quinnwai in #102
- Feature/standardized output rebase by @quinnwai in #109
Full Changelog: https://github.com/gks-anvil/vrs_anvil_toolkit/commits/0.2.0rc5
- Update README.md Logo by @quinnwai in #110
- v0.3.0: Building Cohort Allele Frequency objects with Plugins! by @quinnwai in #111
Full Changelog: 0.2.0rc5...0.3.0
