Filter Qualified Bases

#FilterQualifiedBases

[[step]]
    action = "FilterQualifiedBases"
    min_quality: u8 # the quality value >= which a base is qualified. 
                    # In your phred encoding. Typically 33..75
    max_percentage: the maximum percentage of unqualified bases necessary (0..=1)
    target: Read1|Read2|Index1|Index2

Filter by the maximum percentage of bases that are ‘unqualified’, that is below a threshold.

Corresponding options in other software #

  • fastp : –qualified_quality_phred / –unqualified_percent_limit