Critical regions

How to recreate/update critical regions of proteins and critical regions without benign mutations

Recreate

• Uncomment the respective code section and update paths in GenOtoScope/create_beds4PVS1.py

• Run the updated script and two output files will be created on the subfolder genotoscope_data/annotation_beds/clinvar_version_uniprot_version:

  critical_regions_pathogenic_probability.bed

  critical_regions_pathogenic_probability_no_benign.bed

Update

• Update ClinVar and UniProt open data files to the latest version as explained in ClinVar UniProt
• Select the pathogenic probability threshold in GenOtoScope/beds/FindCriticalProteinRegions/run()
• Apply the "Recreate" steps