#CalcQualifiedBases

[[step]]
    action = "CalcQualifiedBases"
    threshold = 'C' # the quality value >= which a base is qualified 
                    # In your phred encoding. Typically 33..75
                    # a byte or a number 0...255
    op = 'worse' # see below.
    segment = "read1" # Any of your input segments, or 'All'
    out_label = "tag_name"

Calculate the number of bases that are ‘qualified’, that is abov/below a user defined threshold.

Note that smaller Phred values are better.

To remove confusion, op may be ‘Better’/‘Worse’ instead of ‘Below’/‘Above’.

Accepted values for `op= are

• worse / above / > / gt
• worse_or_equal / above_or_equal / >= / gte
• better / below / < / lt
• better_or_equal / below_or_equal / <= / lte

Corresponding options in other software #

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