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Clinical-Genomics-Lund / nextflow_wgs

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Add VEP111 annotations to rank models #183

Closed alkc closed 5 months ago

alkc commented 5 months ago

Description

What is changed? What is the result of the changes?

This update adds new VEP consequences to all deployed rank models:

  [[splice_donor_5th_base_variant]]                  
    score = 5                                        
    priority = 4                                     
    string = 'splice_donor_5th_base_variant'         

  [[splice_donor_region_variant]]                    
    score = 5                                        
    priority = 4                                     
    string = 'splice_donor_region_variant'           

  [[splice_polypyrimidine_tract_variant]]            
    score = 5                                        
    priority = 4                                     
    string = 'splice_polypyrimidine_tract_variant'   

  [[start_retained_variant]]                         
    score = 1                                        
    priority = 2                                     
    string = 'start_retained_variant'                

  [[sequence_variant]]                               
    score = 1                                        
    priority = 0                                     
    string = 'sequence_variant'

Also fixes the filename version for the onco production model.

TODO

Update w/ VEP 105-111 annotations:

Generate new rank models:

Diff against vep103 versions:

Deploy

Type of change

Testing

This change will be tested in the verification branch PR #142