Extract Qualified Bases

#ExtractQualifiedBases

[[step]]
    action = "ExtractQualifiedBases"
    min_quality = 30 # the quality value >= which a base is qualified 
                    # In your phred encoding. Typically 33..75
                    # a byte or a number 0...255
    segment = "read1" # Any of your input segments, or 'All'
    label = "tag_name"

Calculate by the percentage of bases that are ‘unqualified’, that is below a user defined threshold.

Corresponding options in other software #

  • fastp : –qualified_quality_phred / –unqualified_percent_limit (if combined with FilterByNumericTag)