GKS-ClinVar Analysis

An analysis for submitting to the ClinVar Submission API using GA4GH Genomic Knowledge Standards (GKS) data.

Development of a shared, open-source software package for managing these submissions that can be easily configured for use by multiple submitters would be highly impactful as development and adoption of the GKS framework grows.

The work for this tool can be found at https://github.com/clingen-data-model/clinvar-this.

We plan to contribute to ClinVar This to support GKS data stored as JSON files.

ClinVar Submission API

• Documentation: https://www.ncbi.nlm.nih.gov/clinvar/docs/api_http/
• GitHub: https://github.com/ncbi/clinvar/tree/master/submission_api_schema

ClinVar Submission API Analysis

The analysis directory contains example CIViC and VarCat submissions to the test Submission API. This analysis focused on submitting oncogenicitySubmission and clinicalImpactSubmission objects.

Development

Clone the repo and create a virtual environment:

git clone https://github.com/ga4gh/gks-clinvar
cd gks-clinvar
python3 -m venv venv
source venv/bin/activate

Install development dependencies and pre-commit:

python3 -m pip install -r requirements.txt
pre-commit install

Check style with ruff:

python3 -m ruff format && python3 -m ruff check --fix