clingen-data-model / clingen-hail-reports

Performs filtering against gnomAD and ClinVar datasets. Uses Hail to report records with a population FAF above certain thresholds by gene.
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gnomad-frequency-report

Performs filtering against gnomAD and ClinVar datasets. Uses Hail to report records with a population FAF above certain thresholds by gene.

Configuring Hail

To configure Hail, which this project depends on, please see hail-instructions.md.

Running

This can either be utilized via the Jupyter notebook Clingen-Gnomad-FAF-Report.ipynb which can be opened in the Jupyter notebook environment launched in the Hail connect step.

After running the whole notebook, a file, by default called report.tsv, will be output into the same cloud storage directory that the notebook is running in.