Organizing folders

Organize folders before running GenOtoScope

Analysis root path

genotoscope_classify.py and genotoscope_annotate.py need the parameter analysis_root. The user should specify the analysis root path so that it contains at least 2 sub-folders:

• analysis_root/genotoscope_data
• analysis_root/input_gsvars_folder

Folder organization

First, move the genotoscope_data folder outside the code repository folder.

This folder should be placed in an analysis root where genotoscope_data subfolder and vcf and gsvar subfolder are found

Current versions of open data

Ensembl: version 75 (GRCh37/hg19)

ClinVar: version of March 2021

UniProt: version of February 2021

gnomAD: version 2.1 for GRCh37

To re-download or update these open data please see this wiki section