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gks-anvil / vrs_anvil_toolkit

Extract clinical variant interpretations from VCF using GA4GH VRS IDs
MIT License
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feature/metrics-as-CohortAlleleFrequency #65

Closed bwalsh closed 6 days ago

bwalsh commented 8 months ago

As a vrs_anvil user, I need to be able to consume results in an agreed upon form.

https://github.com/ga4gh/va-spec/blob/1.x/schema/va-spec/profiles/caf/json/CohortAlleleFrequency

bwalsh commented 8 months ago

Also here: https://github.com/broadinstitute/gnomad_methods/blob/main/gnomad/utils/annotations.py https://github.com/broadinstitute/gnomad_methods/blob/main/gnomad/utils/annotations.py#L2546

bwalsh commented 8 months ago

https://github.com/ga4gh/va-spec/blob/bbd1c128818ce4093ef222fb0c8c8f211cdd64a8/Modeling/Population%20Frequency/gnomad_study_result_examples_v6_20230126.yml

quinnwai commented 7 months ago

Note: this has been implemented in the 1000g-figure.py script to reproduce the 1000G analysis on Terra, but we may want to formalize this into the package.

quinnwai commented 6 days ago

supersetted by #94