scout/parse/variant/deleteriousness.py
def parse_cadd(variant, transcripts):
    """Check if the cadd phred score is annotated"""
    cadd = 0
    cadd_keys = ['CADD', 'CADD_PHRED']
    for key in cadd_keys:
        cadd = variant.INFO.get(key, 0)
        if cadd:
            return float(cadd)
    
    for transcript in transcripts:
        cadd_entry = transcript.get('cadd')
        if (cadd_entry and cadd_entry > cadd):
            cadd = cadd_entry
    
    return cadd
def parse_cadd(variant, transcripts):
    cadd = 0
    cadd_keys = ['CADD', 'CADD_PHRED']
    for key in cadd_keys:
        cadd = variant.INFO.get(key, 0)
        if cadd:
            return float(cadd)
    
    for transcript in transcripts:
        cadd_entry = transcript.get('cadd')
        if (cadd_entry and cadd_entry > cadd):
            cadd = cadd_entry
    
    return cadd
def parse_cadd ( variant , transcripts ) : cadd = 0 cadd_keys = [ 'CADD' , 'CADD_PHRED' ] for key in cadd_keys : cadd = variant . INFO . get ( key , 0 ) if cadd : return float ( cadd ) for transcript in transcripts : cadd_entry = transcript . get ( 'cadd' ) if ( cadd_entry and cadd_entry > cadd ) : cadd = cadd_entry return cadd
Check if the cadd phred score is annotated
Check if the cadd phred score is annotated