Clinical-Genomics-Lund / nextflow_wgs

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WGS trio rank model misses `FILTER` PASS rule found in wgs SNV single rank model #182

Open alkc opened 5 months ago

alkc commented 5 months ago
[FILTER]                                                        [FILTER]
  field = FILTER                                                  field = FILTER
  data_type = string                                              data_type = string
  category = Variant_call_quality_filter                          category = Variant_call_quality_filter
  record_rule = min                                               record_rule = min
  separators = ';',                                               separators = ';',
  description = The filters for the variant                       description = The filters for the variant

  [[not_reported]]                                                [[not_reported]]
    score = 0                                                       score = 0

  [[pass]]                                                    |   [[pass2]]
    score = 3                                                       score = 3
    priority = 1                                                    priority = 1
    string = '.'                                                    string = '.'

                                                              >   [[pass]]
                                                              >     score = 3
                                                              >     priority = 1
                                                              >     string = 'PASS'
                                                              >

This bug affects mito variants for trios, as those use PASS instead of .