Small VCF Annotation: First Pass w/out Terra Testing - Githubissues

gks-anvil / vrs_anvil_toolkit

Extract clinical variant interpretations from VCF using GA4GH VRS IDs

MIT License

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Small VCF Annotation: First Pass w/out Terra Testing #4

Closed quinnwai closed 9 months ago

quinnwai commented 10 months ago

Current Design

README for setup instructions which includes...
1. activating conda environment for packages
2. setup.sh script to install seqrepo data, and stores variables in a .env file for later use
create unit test in test/ to ensure expected pkl is identical to the new pkl.

Left to Do for Terra

Uncommenting setup code to get latest seqrepo data
Updating the expected pkl, ensuring that all VRS IDs are accounted for
Testing that...
1. the latest seqrepo data can be pulled down
2. multiple pulls of data will retrieve the most recent direction in $SEQREPO_ROOT to test on
3. that the test pass, ie VCF actually annotates VRS IDs for each allele entry

@bwalsh let me know what design change/feedback needs to be incorporated!

bwalsh commented 9 months ago

LGTM 🥇