Clinical significant exons

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Damianos P. Melidis edited this page Nov 22, 2021 · 1 revision

How to recreate/update clinical significant exons

Recreate

Uncomment the respective code section at update paths in GenOtoScope/create_beds4PVS1.py
Run the updated script and the output file will be saved on the subfolder genotoscope_data/annotation_beds/gnomAD_version:

clinical_significant_exons.bed

Update

Update gnomAD version to the latest as explained in gnomAD
Update filtering method for pLoF accounted for an exon in GenOtoScope/beds/FindClinicalSignificantExons/quality_filter_variants()
Apply the "Recreate" steps

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